{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.platform = \"ILLUMINA\" and tissue_curation = \"Cell Line\"", "rows": [[28458, "SRR26265233", "SRX21974767", "SRS19050630", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN4 2", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFND2", "IFND2", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN4-2.R2.fq.gz IFN4-2.R1.fq.gz", "fastq fastq", 6934783900.0, 23533465.0, "IFN4 2.R1.fq.gz", "0:147.35 1:147.33", "A:1868083790;C:1590902416;G:1598661179;T:1876555558;N:580957", 147, 147, null, null, 1868083790, 1590902416, 1598661179, 1876555558, 580957, "SRX21974767", "SRS19050630", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95226, 0.95256, 0.09237, 0.09199, 0.73403, 0.73472, 0.50112, 0.4946, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28459, "SRR26265234", "SRX21974766", "SRS19050629", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN4 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFND1", "IFND1", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN4-1.R2.fq.gz IFN4-1.R1.fq.gz", "fastq fastq", 6955503146.0, 23557276.0, "IFN4 1.R1.fq.gz", "0:147.65 1:147.61", "A:1873984869;C:1595727817;G:1603714470;T:1881209728;N:866262", 147, 147, null, null, 1873984869, 1595727817, 1603714470, 1881209728, 866262, "SRX21974766", "SRS19050629", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95329, 0.95472, 0.09371, 0.09311, 0.73535, 0.7362, 0.49542, 0.49872, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28460, "SRR26265235", "SRX21974765", "SRS19050628", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN1 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFNA4", "IFNA4", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN1-4.R1.fq.gz IFN1-4.R2.fq.gz", "fastq fastq", 6497442039.0, 22025966.0, "IFN1 4.R1.fq.gz", "0:147.50 1:147.49", "A:1752434033;C:1488528327;G:1495225910;T:1760699235;N:554534", 147, 147, null, null, 1752434033, 1488528327, 1495225910, 1760699235, 554534, "SRX21974765", "SRS19050628", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95168, 0.95288, 0.09073, 0.09058, 0.73691, 0.73697, 0.49659, 0.49706, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28461, "SRR26265236", "SRX21974764", "SRS19050627", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN1 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFNA3", "IFNA3", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN1-3.R1.fq.gz IFN1-3.R2.fq.gz", "fastq fastq", 6258791362.0, 21164255.0, "IFN1 3.R1.fq.gz", "0:147.88 1:147.85", "A:1687323085;C:1434335716;G:1441365307;T:1695236268;N:530986", 147, 147, null, null, 1687323085, 1434335716, 1441365307, 1695236268, 530986, "SRX21974764", "SRS19050627", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95206, 0.95262, 0.09255, 0.09194, 0.73549, 0.73503, 0.49685, 0.50433, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28462, "SRR26265237", "SRX21974763", "SRS19050626", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN1 2", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFNA2", "IFNA2", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN1-2.R1.fq.gz IFN1-2.R2.fq.gz", "fastq fastq", 5566110483.0, 18875664.0, "IFN1 2.R1.fq.gz", "0:147.46 1:147.43", "A:1498457518;C:1278011392;G:1284254482;T:1504942516;N:444575", 147, 147, null, null, 1498457518, 1278011392, 1284254482, 1504942516, 444575, "SRX21974763", "SRS19050626", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95197, 0.9524, 0.09035, 0.08962, 0.73606, 0.73634, 0.50146, 0.49994, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28463, "SRR26265238", "SRX21974762", "SRS19050625", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN1 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFNA1", "IFNA1", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN1-1.R1.fq.gz IFN1-1.R2.fq.gz", "fastq fastq", 6919610192.0, 23425305.0, "IFN1 1.R1.fq.gz", "0:147.71 1:147.68", "A:1863998722;C:1587286271;G:1595557648;T:1872190552;N:576999", 147, 147, null, null, 1863998722, 1587286271, 1595557648, 1872190552, 576999, "SRX21974762", "SRS19050625", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95297, 0.95392, 0.08926, 0.0886, 0.73744, 0.73716, 0.48737, 0.49536, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28464, "SRR26265239", "SRX21974761", "SRS19050624", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "Control 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "C4", "C4", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "Control-4.R1.fq.gz Control-4.R2.fq.gz", "fastq fastq", 7048754711.0, 23843338.0, "Control 4.R1.fq.gz", "0:147.83 1:147.80", "A:1886695953;C:1629137936;G:1637672845;T:1894536437;N:711540", 147, 147, null, null, 1886695953, 1629137936, 1637672845, 1894536437, 711540, "SRX21974761", "SRS19050624", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.9556, 0.95723, 0.09014, 0.08984, 0.73533, 0.73643, 0.50146, 0.50134, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28465, "SRR26265240", "SRX21974760", "SRS19050623", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "Control 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "C3", "C3", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "Control-3.R1.fq.gz Control-3.R2.fq.gz", "fastq fastq", 6936430397.0, 23495179.0, "Control 3.R1.fq.gz", "0:147.63 1:147.60", "A:1861679698;C:1598594022;G:1606747561;T:1868699697;N:709419", 147, 147, null, null, 1861679698, 1598594022, 1606747561, 1868699697, 709419, "SRX21974760", "SRS19050623", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95496, 0.95472, 0.09092, 0.08958, 0.73505, 0.73586, 0.50541, 0.50256, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28466, "SRR26265241", "SRX21974759", "SRS19050622", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN4 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFND4", "IFND4", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN4-4.R1.fq.gz IFN4-4.R2.fq.gz", "fastq fastq", 6904025687.0, 23391394.0, "IFN4 4.R1.fq.gz", "0:147.59 1:147.56", "A:1858866141;C:1585020535;G:1592940944;T:1866550686;N:647381", 147, 147, null, null, 1858866141, 1585020535, 1592940944, 1866550686, 647381, "SRX21974759", "SRS19050622", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95345, 0.95394, 0.08901, 0.08834, 0.73537, 0.73596, 0.50012, 0.49674, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28467, "SRR26265242", "SRX21974758", "SRS19050621", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "IFN4 3", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "IFND3", "IFND3", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "IFN4-3.R1.fq.gz IFN4-3.R2.fq.gz", "fastq fastq", 6983243474.0, 23627912.0, "IFN4 3.R1.fq.gz", "0:147.80 1:147.75", "A:1880838380;C:1603492441;G:1611871993;T:1885974103;N:1066557", 147, 147, null, null, 1880838380, 1603492441, 1611871993, 1885974103, 1066557, "SRX21974758", "SRS19050621", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95262, 0.95399, 0.09442, 0.09269, 0.73586, 0.73519, 0.50113, 0.49912, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28468, "SRR26265243", "SRX21974757", "SRS19050620", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "Control 2", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "C2", "C2", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "Control-2.R1.fq.gz Control-2.R2.fq.gz", "fastq fastq", 7064416471.0, 23901145.0, "Control 2.R1.fq.gz", "0:147.80 1:147.77", "A:1896430007;C:1626943513;G:1635235356;T:1905174563;N:633032", 147, 147, null, null, 1896430007, 1626943513, 1635235356, 1905174563, 633032, "SRX21974757", "SRS19050620", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95546, 0.95678, 0.08984, 0.08994, 0.73535, 0.73565, 0.49891, 0.49705, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28469, "SRR26265244", "SRX21974756", "SRS19050619", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.", null, null, null, null, "Control 1", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "C1", "C1", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464312", null, null, "Control-1.R1.fq.gz Control-1.R2.fq.gz", "fastq fastq", 7005585889.0, 23733330.0, "Control 1.R1.fq.gz", "0:147.61 1:147.57", "A:1874251473;C:1620035540;G:1628125464;T:1882607735;N:565677", 147, 147, null, null, 1874251473, 1620035540, 1628125464, 1882607735, 565677, "SRX21974756", "SRS19050619", "SRA1725060", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 2, 0.95539, 0.95612, 0.08699, 0.08663, 0.73777, 0.73833, 0.49693, 0.49816, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-03", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [30692, "SRR29655998", "SRX25159999", "SRS21850513", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC145382 HuNoV infected  replicate 1  scRNAseq", "GSM8370069", null, "tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC145382 HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger", "Tg mpeg:mCherry", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected", "GSM8370069", "GSM8370069: GC145382 HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8370069 r1", "GSM8370069", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC145382_SI-GA-B1_S1_L001_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L001_R2_001.fastq.gz", "fastq fastq", 5781664526.0, 48997157.0, "GSM8370069 r1", "0:28 1:90", "A:1659071356;C:1268706433;G:1342749232;T:1510681009;N:456496", 28, 90, null, null, 1659071356, 1268706433, 1342749232, 1510681009, 456496, "SRX25159999", "SRS21850513", "SRA1913292", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-06-30", "Larval", "Larval", "Cell Line", "Cell Line"], [30693, "SRR29655999", "SRX25159999", "SRS21850513", "SRP494129", "PRJNA1085664", "Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile", "GSE261163", "Transcriptome Analysis", "Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.", null, "pubmed:39584740", null, "GC145382 HuNoV infected  replicate 1  scRNAseq", "GSM8370069", null, "tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing", "GC145382 HuNoV infected  replicate 1  scRNAseq", "Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger", "Tg mpeg:mCherry", null, "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 protocol.", null, "cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected", "GSM8370069", "GSM8370069: GC145382 HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM8370069 r1", "GSM8370069", "1", "Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 \u00b5g/mL proteinase K  0.25% trypsin for 40 min at 37\u00b0C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494129", null, null, "GC145382_SI-GA-B1_S1_L002_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L002_R2_001.fastq.gz", "fastq fastq", 6046508328.0, 51241596.0, "GSM8370069 r2", "0:28 1:90", "A:1731027394;C:1330440539;G:1408717533;T:1575870623;N:452239", 28, 90, null, null, 1731027394, 1330440539, 1408717533, 1575870623, 452239, "SRX25159999", "SRS21850513", "SRA1913292", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", "Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-06-30", "Larval", "Larval", "Cell Line", "Cell Line"], [33982, "SRR31022893", "SRX26409990", "SRS22929902", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat four:the PTA solution was exposed and cultured ttwo xxxdpf", "PTA", "PTA4", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "PTA4", "PTA4", "Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich  Massachusetts  USA to construct sequencing libraries.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539058", null, null, "PTA4_R1.fastq.gz PTA4_R2.fastq.gz", "fastq fastq", 8283122214.0, 27427557.0, "PTA4 R1.fastq.gz", "0:151 1:151", "A:2240001804;C:1891821306;G:1934930549;T:2215819380;N:549175", 151, 151, null, null, 2240001804, 1891821306, 1934930549, 2215819380, 549175, "SRX26409990", "SRS22929902", "SRA1992822", "Nanchang University|College of Life Science", "Nanchang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-10-17", "Larval", "Larval", "Cell Line", "Cell Line"], [33983, "SRR31022894", "SRX26409989", "SRS22929901", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat three:the PTA solution was exposed and cultured ttwo xxxdpf", "PTA", "PTA3", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "PTA3", "PTA3", "Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich  Massachusetts  USA to construct sequencing libraries.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539058", null, null, "PTA3_R1.fastq.gz PTA3_R2.fastq.gz", "fastq fastq", 7022708604.0, 23254002.0, "PTA3 R1.fastq.gz", "0:151 1:151", "A:1891728501;C:1605352134;G:1649370849;T:1875796526;N:460594", 151, 151, null, null, 1891728501, 1605352134, 1649370849, 1875796526, 460594, "SRX26409989", "SRS22929901", "SRA1992822", "Nanchang University|College of Life Science", "Nanchang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-10-17", "Larval", "Larval", "Cell Line", "Cell Line"], [33984, "SRR31022895", "SRX26409988", "SRS22929900", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat two:the PTA solution was exposed and cultured ttwo xxxdpf", "PTA", "PTA2", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "PTA2", "PTA2", "Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich  Massachusetts  USA to construct sequencing libraries.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539058", null, null, "PTA2_R1.fastq.gz PTA2_R2.fastq.gz", "fastq fastq", 7096338016.0, 23497808.0, "PTA2 R1.fastq.gz", "0:151 1:151", "A:1934868395;C:1599522000;G:1643956349;T:1917509746;N:481526", 151, 151, null, null, 1934868395, 1599522000, 1643956349, 1917509746, 481526, "SRX26409988", "SRS22929900", "SRA1992822", "Nanchang University|College of Life Science", "Nanchang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-10-17", "Larval", "Larval", "Cell Line", "Cell Line"], [33985, "SRR31022896", "SRX26409987", "SRS22929899", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat one:the PTA solution was exposed and cultured ttwo xxxdpf", "PTA", "PTA1", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "PTA1", "PTA1", "Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich  Massachusetts  USA to construct sequencing libraries.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539058", null, null, "PTA1_R1.fastq.gz PTA1_R2.fastq.gz", "fastq fastq", 7610150246.0, 25199173.0, "PTA1 R1.fastq.gz", "0:151 1:151", "A:2078407024;C:1716455571;G:1761054093;T:2053740332;N:493226", 151, 151, null, null, 2078407024, 1716455571, 1761054093, 2053740332, 493226, "SRX26409987", "SRS22929899", "SRA1992822", "Nanchang University|College of Life Science", "Nanchang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-10-17", "Larval", "Larval", "Cell Line", "Cell Line"], [33986, "SRR31022897", "SRX26409986", "SRS22929896", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat four:culture medium to 4dpf for sample collection", "Control", "Control4", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "Control4", "Control4", "Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich  Massachusetts  USA to construct sequencing libraries.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539058", null, null, "Control4_R1.fastq.gz Control4_R2.fastq.gz", "fastq fastq", 9023764832.0, 29880016.0, "Control4 R1.fastq.gz", "0:151 1:151", "A:2384249866;C:2111349516;G:2165103194;T:2362466565;N:595691", 151, 151, null, null, 2384249866, 2111349516, 2165103194, 2362466565, 595691, "SRX26409986", "SRS22929896", "SRA1992822", "Nanchang University|College of Life Science", "Nanchang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-10-17", "Larval", "Larval", "Cell Line", "Cell Line"], [33987, "SRR31022898", "SRX26409985", "SRS22929898", "SRP539058", "PRJNA1173962", "Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution", "PRJNA1173962", "Other", "ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat three:culture medium to 4dpf for sample collection", "Control", "Control3", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "Control3", "Control3", "Use the Invitrogen TRIzol kit to extract total RNA. 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Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat two:culture medium to 4dpf for sample collection", "Control", "Control2", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "Control2", "Control2", "Use the Invitrogen TRIzol kit to extract total RNA. 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Due to its high water solubility and more negative reports on aquatic organisms in recent yrs  it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study  the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.", null, null, "Repeat one:culture medium to 4dpf for sample collection", "Control", "Control1", null, "strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "Control1", "Control1", "Use the Invitrogen TRIzol kit to extract total RNA. 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Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "Ca-3_merge.R1.fastq.gz Ca-3_merge.R2.fastq.gz", "fastq fastq", 6737357100.0, 22457857.0, "Ca 3 merge.R1.fastq.gz", "0:150 1:150", "A:1838531075;C:1527684677;G:1561100877;T:1809740217;N:300254", 150, 150, null, null, 1838531075, 1527684677, 1561100877, 1809740217, 300254, "SRX28641175", "SRS24911532", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [36008, "SRR33398627", "SRX28641174", "SRS24911531", "SRP582620", "PRJNA1256937", "Transcriptome data of zebrafish", "PRJNA1256937", "Other", "Zebrafish larvae were treated with carbimazole until 120 hpf  aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish", null, null, "not collected", null, "Ca 2", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 20|geo loc name:China: Fujian  Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University  School of Biological Science and Engineering  Institute of Life Sciences  Room 211|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "Ca2", "Ca2", "First  sample collection and processing the samples are from 5 dpf juvenile fish. Second  conduct RNA extraction and quality detection. Then  construct the library and perform sequencing on the machine. Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "Ca-2_merge.R1.fastq.gz Ca-2_merge.R2.fastq.gz", "fastq fastq", 7269644400.0, 24232148.0, "Ca 2 merge.R1.fastq.gz", "0:150 1:150", "A:1977905783;C:1657807837;G:1689935893;T:1943719982;N:274905", 150, 150, null, null, 1977905783, 1657807837, 1689935893, 1943719982, 274905, "SRX28641174", "SRS24911531", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [36009, "SRR33398628", "SRX28641173", "SRS24911530", "SRP582620", "PRJNA1256937", "Transcriptome data of zebrafish", "PRJNA1256937", "Other", "Zebrafish larvae were treated with carbimazole until 120 hpf  aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish", null, null, "not collected", null, "Ca 1", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 19|geo loc name:China: Fujian  Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University  School of Biological Science and Engineering  Institute of Life Sciences  Room 210|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "Ca1", "Ca1", "First  sample collection and processing the samples are from 5 dpf juvenile fish. Second  conduct RNA extraction and quality detection. Then  construct the library and perform sequencing on the machine. Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "Ca-1_merge.R1.fastq.gz Ca-1_merge.R2.fastq.gz", "fastq fastq", 7116911700.0, 23723039.0, "Ca 1 merge.R1.fastq.gz", "0:150 1:150", "A:1950685415;C:1604814494;G:1640315886;T:1920831569;N:264336", 150, 150, null, null, 1950685415, 1604814494, 1640315886, 1920831569, 264336, "SRX28641173", "SRS24911530", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [36010, "SRR33398629", "SRX28641172", "SRS24911529", "SRP582620", "PRJNA1256937", "Transcriptome data of zebrafish", "PRJNA1256937", "Other", "Zebrafish larvae were treated with carbimazole until 120 hpf  aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish", null, null, "not collected", null, "WT 3", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 18|geo loc name:China: Fujian  Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University  School of Biological Science and Engineering  Institute of Life Sciences  Room 209|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "WT3", "WT3", "First  sample collection and processing the samples are from 5 dpf juvenile fish. Second  conduct RNA extraction and quality detection. Then  construct the library and perform sequencing on the machine. Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "WT-3_merge.R1.fastq.gz WT-3_merge.R2.fastq.gz", "fastq fastq", 6806732100.0, 22689107.0, "WT 3 merge.R1.fastq.gz", "0:150 1:150", "A:1844325028;C:1558003481;G:1585120438;T:1819030091;N:253062", 150, 150, null, null, 1844325028, 1558003481, 1585120438, 1819030091, 253062, "SRX28641172", "SRS24911529", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [36011, "SRR33398630", "SRX28641171", "SRS24911528", "SRP582620", "PRJNA1256937", "Transcriptome data of zebrafish", "PRJNA1256937", "Other", "Zebrafish larvae were treated with carbimazole until 120 hpf  aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish", null, null, "not collected", null, "WT 2", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 17|geo loc name:China: Fujian  Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University  School of Biological Science and Engineering  Institute of Life Sciences  Room 208|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "WT2", "WT2", "First  sample collection and processing the samples are from 5 dpf juvenile fish. Second  conduct RNA extraction and quality detection. Then  construct the library and perform sequencing on the machine. Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "WT-2_merge.R1.fastq.gz WT-2_merge.R2.fastq.gz", "fastq fastq", 9350997600.0, 31169992.0, "WT 2 merge.R1.fastq.gz", "0:150 1:150", "A:2531840914;C:2136380344;G:2177743101;T:2504682606;N:350635", 150, 150, null, null, 2531840914, 2136380344, 2177743101, 2504682606, 350635, "SRX28641171", "SRS24911528", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [36012, "SRR33398631", "SRX28641170", "SRS24911527", "SRP582620", "PRJNA1256937", "Transcriptome data of zebrafish", "PRJNA1256937", "Other", "Zebrafish larvae were treated with carbimazole until 120 hpf  aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish", null, null, "not collected", null, "WT 1", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 16|geo loc name:China: Fujian  Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University  School of Biological Science and Engineering  Institute of Life Sciences  Room 207|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "WT1", "WT1", "First  sample collection and processing the samples are from 5 dpf juvenile fish. Second  conduct RNA extraction and quality detection. Then  construct the library and perform sequencing on the machine. Finally  carry out data analysis.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582620", null, null, "WT-1_merge.R1.fastq.gz WT-1_merge.R2.fastq.gz", "fastq fastq", 8025342600.0, 26751142.0, "WT 1 merge.R1.fastq.gz", "0:150 1:150", "A:2210250425;C:1804024657;G:1840044555;T:2170729304;N:293659", 150, 150, null, null, 2210250425, 1804024657, 1840044555, 2170729304, 293659, "SRX28641170", "SRS24911527", "SRA2121261", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University", "Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-01", "Larval", "Larval", "Cell Line", "Cell Line"], [44943, "SRR6324387", "SRX3424140", "SRS2715772", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 18 30d rep3", "GSM2865571", null, "tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "ZF4 18 30d rep3", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 18 30d", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "GSM2865571", "GSM2865571: ZF4 18 30d rep3; Danio rerio; RNA Seq", "GSM2865571", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865571", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "6_1.fq.gz 6_2.fq.gz", "fastq fastq", 8502006300.0, 28340021.0, "GSM2865571 r1", "0:150 1:150", "A:2222321266;C:2022701531;G:2022825678;T:2234014077;N:143748", 150, 150, null, null, 2222321266, 2022701531, 2022825678, 2234014077, 143748, "SRX3424140", "SRS2715772", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.92868, 0.92895, 0.15866, 0.15599, 0.74146, 0.74505, 0.49577, 0.49894, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [44944, "SRR6324386", "SRX3424139", "SRS2715771", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 18 30d rep2", "GSM2865570", null, "tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "ZF4 18 30d rep2", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 18 30d", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "GSM2865570", "GSM2865570: ZF4 18 30d rep2; Danio rerio; RNA Seq", "GSM2865570", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865570", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "4_1.fq.gz 4_2.fq.gz", "fastq fastq", 8571202200.0, 28570674.0, "GSM2865570 r1", "0:150 1:150", "A:2268978542;C:2005726985;G:2030919273;T:2265431269;N:146131", 150, 150, null, null, 2268978542, 2005726985, 2030919273, 2265431269, 146131, "SRX3424139", "SRS2715771", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.92516, 0.92417, 0.18269, 0.17989, 0.73352, 0.73813, 0.51554, 0.50598, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [44945, "SRR6324385", "SRX3424138", "SRS2715770", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 18 30d rep1", "GSM2865569", null, "tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "ZF4 18 30d rep1", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 18 30d", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18\u00b0C for 30 days|sample group:cold treatment for 30 days", "GSM2865569", "GSM2865569: ZF4 18 30d rep1; Danio rerio; RNA Seq", "GSM2865569", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865569", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "2_1.fq.gz 2_2.fq.gz", "fastq fastq", 9855530100.0, 32851767.0, "GSM2865569 r1", "0:150 1:150", "A:2584345651;C:2339107553;G:2359863664;T:2572047288;N:165944", 150, 150, null, null, 2584345651, 2339107553, 2359863664, 2572047288, 165944, "SRX3424138", "SRS2715770", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.92395, 0.92354, 0.18307, 0.17869, 0.73667, 0.74199, 0.52681, 0.53689, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [44946, "SRR6324384", "SRX3424137", "SRS2715768", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 28 rep3", "GSM2865568", null, "tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "ZF4 28 rep3", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 28", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "GSM2865568", "GSM2865568: ZF4 28 rep3; Danio rerio; RNA Seq", "GSM2865568", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865568", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "5_1.fq.gz 5_2.fq.gz", "fastq fastq", 6344338200.0, 21147794.0, "GSM2865568 r1", "0:150 1:150", "A:1726699573;C:1445357744;G:1438849187;T:1733324130;N:107566", 150, 150, null, null, 1726699573, 1445357744, 1438849187, 1733324130, 107566, "SRX3424137", "SRS2715768", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.9124, 0.91371, 0.29012, 0.28803, 0.73525, 0.74038, 0.53934, 0.55133, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [44947, "SRR6324383", "SRX3424136", "SRS2715767", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 28 rep2", "GSM2865567", null, "tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "ZF4 28 rep2", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 28", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "GSM2865567", "GSM2865567: ZF4 28 rep2; Danio rerio; RNA Seq", "GSM2865567", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865567", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "3_1.fq.gz 3_2.fq.gz", "fastq fastq", 7909395600.0, 26364652.0, "GSM2865567 r1", "0:150 1:150", "A:2096969069;C:1849259032;G:1867407953;T:2095652151;N:107395", 150, 150, null, null, 2096969069, 1849259032, 1867407953, 2095652151, 107395, "SRX3424136", "SRS2715767", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.90044, 0.89889, 0.19795, 0.1953, 0.73898, 0.74182, 0.5238, 0.52236, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [44948, "SRR6324382", "SRX3424135", "SRS2715769", "SRP125677", "PRJNA419909", "Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE107369", "Transcriptome Analysis", "Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far  no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28\u00b0C as control with that of cold acclimated cells cultured at 18\u00b0C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs  there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells  compared with that of control cells at 28\u00b0C. Among differentially expressed lncRNAs  74 and 61 were found only in control cells or in cold acclimated cells  respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport  cell adhesion  oxidation reduction process  and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA  and constructed a complex interaction network. In summary  our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells  lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:29634734", null, "ZF4 28 rep1", "GSM2865566", null, "tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "ZF4 28 rep1", "Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter \u201c G Danio rerio.GRCz10.88.gtf\u201d all assemblies were merged together utilizing StringTie\u2019s \u201cmerge\u201d function CPC Coding Potential Calculator  CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The  genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs", "ZF4 28", "For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini  1993.  The cells were grown at 28 \u00b0C  5% CO2  in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS  1% l glutamine  100 u/ml penicillin  100 \u03bcg/ml streptomycin.  For cold treatment  cells were grown at 18 \u00b0C  5% CO2  in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA.", "cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28\u00b0C|sample group:control", "GSM2865566", "GSM2865566: ZF4 28 rep1; Danio rerio; RNA Seq", "GSM2865566", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302  Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM2865566", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP125677", null, null, "1_2.fq.gz 1_1.fq.gz", "fastq fastq", 9364351500.0, 31214505.0, "GSM2865566 r1", "0:150 1:150", "A:2483908747;C:2191875885;G:2204013829;T:2484392803;N:160236", 150, 150, null, null, 2483908747, 2191875885, 2204013829, 2484392803, 160236, "SRX3424135", "SRS2715769", "SRA634103", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 2, 0.91474, 0.91441, 0.21056, 0.20796, 0.739, 0.74477, 0.52778, 0.53276, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "China", "2017-11-27", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [49815, "SRR8987978", "SRX5767074", "SRS4701368", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "24h 6", "sample exposed to microcystin for xxxh   replicate #6", null, "ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh   replicate #6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to  microcystin for xxxh   replicate #6", "24h 3", "24h 3", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h3_clean_R2.fq.gz 24h3_clean_R1.fq.gz", "fastq fastq", 6275458528.0, 20779664.0, "24h3 clean R1.fq.gz", "0:151 1:151", "A:1685303886;C:1437291030;G:1447147160;T:1702856463;N:2859989", 151, 151, null, null, 1685303886, 1437291030, 1447147160, 1702856463, 2859989, "SRX5767074", "SRS4701368", "SRA880742", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92675, 0.92679, 0.13415, 0.13431, 0.73945, 0.74213, 0.50477, 0.50726, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49816, "SRR8987979", "SRX5767073", "SRS4701367", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "24h 4", "sample exposed to microcystin for xxxh   replicate #4", null, "ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh   replicate #4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to  microcystin for xxxh   replicate #4", "24h 1", "24h 1", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h1_clean_R1.fq.gz 24h1_clean_R2.fq.gz", "fastq fastq", 6373552356.0, 21104478.0, "24h1 clean R1.fq.gz", "0:151 1:151", "A:1712827186;C:1458408871;G:1470508604;T:1728973011;N:2834684", 151, 151, null, null, 1712827186, 1458408871, 1470508604, 1728973011, 2834684, "SRX5767073", "SRS4701367", "SRA880742", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9248, 0.92582, 0.13207, 0.13239, 0.73839, 0.74038, 0.49865, 0.50119, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49817, "SRR8987980", "SRX5767072", "SRS4701366", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "24h 5", "sample exposed to microcystin for xxxh   replicate #5", null, "ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh   replicate #5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to  microcystin for xxxh   replicate #5", "24h 2", "24h 2", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h2_clean_R2.fq.gz 24h2_clean_R1.fq.gz", "fastq fastq", 6303822066.0, 20873583.0, "24h2 clean R1.fq.gz", "0:151 1:151", "A:1694366688;C:1441733171;G:1453717629;T:1711017538;N:2987040", 151, 151, null, null, 1694366688, 1441733171, 1453717629, 1711017538, 2987040, "SRX5767072", "SRS4701366", "SRA880742", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9264, 0.92591, 0.13121, 0.13204, 0.7385, 0.74227, 0.50323, 0.49357, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49818, "SRR8983315", "SRX5762615", "SRS4697269", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "12h 5", "sample exposed to microcystin for xxxh   replicate #5", null, "ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh   replicate #5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to  microcystin for xxxh   replicate #5", "12h 5", "12h 5", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. 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The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "1h2_clean_R2.fq.gz 1h2_clean_R1.fq.gz", "fastq fastq", 5616651266.0, 18598183.0, "1h2 clean R1.fq.gz", "0:151 1:151", "A:1492544948;C:1296049637;G:1317613246;T:1507292547;N:3150888", 151, 151, null, null, 1492544948, 1296049637, 1317613246, 1507292547, 3150888, "SRX5740638", "SRS4676159", "SRA879791", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93168, 0.93082, 0.12771, 0.12751, 0.75653, 0.75964, 0.508, 0.51051, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49830, "SRR8959882", "SRX5739436", "SRS4675912", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #6", "ck 6", null, "replicate:replicate=#6|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 6", "ck 6", "ck 6", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. 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The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK3_clean_R1.fq.gz CK3_clean_R2.fq.gz", "fastq fastq", 6417346282.0, 21249491.0, "CK3 clean R1.fq.gz", "0:151 1:151", "A:1753073270;C:1445910840;G:1452693305;T:1762084157;N:3584710", 151, 151, null, null, 1753073270, 1445910840, 1452693305, 1762084157, 3584710, "SRX5739436", "SRS4675912", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92653, 0.92662, 0.11696, 0.11682, 0.75166, 0.75379, 0.50678, 0.50594, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49831, "SRR8959883", "SRX5739435", "SRS4675911", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #4", "ck 4", null, "replicate:replicate=#4|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 4", "ck 4", "ck 4", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK1_clean_R1.fq.gz CK1_clean_R2.fq.gz", "fastq fastq", 5659831830.0, 18741165.0, "CK1 clean R1.fq.gz", "0:151 1:151", "A:1532952307;C:1289729700;G:1295220307;T:1538761250;N:3168266", 151, 151, null, null, 1532952307, 1289729700, 1295220307, 1538761250, 3168266, "SRX5739435", "SRS4675911", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92518, 0.92535, 0.11332, 0.11378, 0.74919, 0.75235, 0.50223, 0.49803, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49832, "SRR8959884", "SRX5739434", "SRS4675910", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #5", "ck 5", null, "replicate:replicate=#5|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 5", "ck 5", "ck 5", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK2_clean_R1.fq.gz CK2_clean_R2.fq.gz", "fastq fastq", 5880727616.0, 19472608.0, "CK2 clean R1.fq.gz", "0:151 1:151", "A:1575999691;C:1352057289;G:1366253556;T:1583120335;N:3296745", 151, 151, null, null, 1575999691, 1352057289, 1366253556, 1583120335, 3296745, "SRX5739434", "SRS4675910", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93653, 0.9349, 0.09037, 0.09026, 0.76262, 0.76572, 0.51143, 0.50376, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49833, "SRR8133154", "SRX4954244", "SRS3995636", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "24h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #1", "24h 1", "24h 1", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-1_R1.fastq.gz 24h-1_R2.fastq.gz", "fastq fastq", 6408674352.0, 21220776.0, "24h 1 R1.fastq.gz", "0:151 1:151", "A:1752104547;C:1447174976;G:1451968217;T:1757298923;N:127689", 151, 151, null, null, 1752104547, 1447174976, 1451968217, 1757298923, 127689, "SRX4954244", "SRS3995636", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9212, 0.91969, 0.14419, 0.14446, 0.73677, 0.74363, 0.49228, 0.49725, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-30", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49834, "SRR8133155", "SRX4954243", "SRS3995635", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "24h 2", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "24h 2", "24h 2", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-2_R1.fastq.gz 24h-2_R2.fastq.gz", "fastq fastq", 6331528754.0, 20965327.0, "24h 2 R1.fastq.gz", "0:151 1:151", "A:1725083256;C:1436372645;G:1442486884;T:1727457912;N:128057", 151, 151, null, null, 1725083256, 1436372645, 1442486884, 1727457912, 128057, "SRX4954243", "SRS3995635", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92281, 0.92303, 0.13905, 0.14045, 0.73708, 0.74401, 0.50843, 0.50295, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49835, "SRR8133156", "SRX4954242", "SRS3995634", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "24h 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "24h 3", "24h 3", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-3_R1.fastq.gz 24h-3_R2.fastq.gz", "fastq fastq", 6723114940.0, 22261970.0, "24h 3 R1.fastq.gz", "0:151 1:151", "A:1833689339;C:1522824611;G:1529534136;T:1836931192;N:135662", 151, 151, null, null, 1833689339, 1522824611, 1529534136, 1836931192, 135662, "SRX4954242", "SRS3995634", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.91356, 0.91347, 0.13955, 0.14059, 0.73898, 0.74399, 0.49776, 0.50087, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49836, "SRR8133151", "SRX4954241", "SRS3995633", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "12h 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "12h 3", "12h 3", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "12h-3_R1.fastq.gz 12h-3_R2.fastq.gz", "fastq fastq", 6249709404.0, 20694402.0, "12h 3 R1.fastq.gz", "0:151 1:151", "A:1679876276;C:1439210018;G:1449953029;T:1680544537;N:125544", 151, 151, null, null, 1679876276, 1439210018, 1449953029, 1680544537, 125544, "SRX4954241", "SRS3995633", "SRA800476", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9318, 0.93185, 0.10315, 0.10397, 0.7499, 0.75513, 0.49669, 0.50516, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49837, "SRR8133152", "SRX4954240", "SRS3995632", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "12h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #1", "12h 1", "12h 1", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. 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Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "6h-3_R1.fastq.gz 6h-3_R2.fastq.gz", "fastq fastq", 6533368340.0, 21633670.0, "6h 3 R1.fastq.gz", "0:151 1:151", "A:1684379253;C:1575728468;G:1593737205;T:1678875387;N:648027", 151, 151, null, null, 1684379253, 1575728468, 1593737205, 1678875387, 648027, "SRX4953863", "SRS3995402", "SRA800451", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.94744, 0.94959, 0.06681, 0.06774, 0.76459, 0.77711, 0.4873, 0.49779, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49840, "SRR8132756", "SRX4953862", "SRS3995403", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "6h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #1", "6h 1", "6h 1", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "6h-1_R1.fastq.gz 6h-1_R2.fastq.gz", "fastq fastq", 6686156482.0, 22139591.0, "6h 1 R1.fastq.gz", "0:151 1:151", "A:1712757343;C:1622803789;G:1646819107;T:1703094369;N:681874", 151, 151, null, null, 1712757343, 1622803789, 1646819107, 1703094369, 681874, "SRX4953862", "SRS3995403", "SRA800449", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.95018, 0.95234, 0.0661, 0.06774, 0.77268, 0.78652, 0.49287, 0.48663, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49841, "SRR8132755", "SRX4953861", "SRS3995401", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "6h 2", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #2", "6h 2", "6h 2", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "6h-2_R1.fastq.gz 6h-2_R2.fastq.gz", "fastq fastq", 5551304204.0, 18381802.0, "6h 2 R1.fastq.gz", "0:151 1:151", "A:1408740987;C:1361721973;G:1380328727;T:1399965481;N:547036", 151, 151, null, null, 1408740987, 1361721973, 1380328727, 1399965481, 547036, "SRX4953861", "SRS3995401", "SRA800450", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9506, 0.95313, 0.07031, 0.07155, 0.7739, 0.78591, 0.50125, 0.49851, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49842, "SRR8119911", "SRX4946208", "SRS3988532", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "3h 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #3", "3h 3", "3h 3", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "3h-3_R1.fastq.gz 3h-3_R2.fastq.gz", "fastq fastq", 6249422202.0, 20693451.0, "3h 3 R1.fastq.gz", "0:151 1:151", "A:1700610088;C:1416827975;G:1436930329;T:1694433965;N:619845", 151, 151, null, null, 1700610088, 1416827975, 1436930329, 1694433965, 619845, "SRX4946208", "SRS3988532", "SRA799983", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.924, 0.92633, 0.13412, 0.13864, 0.74158, 0.76489, 0.49551, 0.49903, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-29", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49843, "SRR8119910", "SRX4946207", "SRS3988531", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "3h 2", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #2", "3h 2", "3h 2", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "3h-2_R1.fastq.gz 3h-2_R2.fastq.gz", "fastq fastq", 6691460508.0, 22157154.0, "3h 2 R2.fastq.gz", "0:151 1:151", "A:1817827404;C:1520902100;G:1534921644;T:1817122657;N:686703", 151, 151, null, null, 1817827404, 1520902100, 1534921644, 1817122657, 686703, "SRX4946207", "SRS3988531", "SRA799982", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92541, 0.92734, 0.13003, 0.1321, 0.7443, 0.76019, 0.50143, 0.4998, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49844, "SRR8117643", "SRX4943940", "SRS3986328", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "3h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #1", "3h 1", "3h 1", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. 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The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "1h-2_R1.fastq.gz 1h-2_R2.fastq.gz", "fastq fastq", 7594153306.0, 25146203.0, "1h 2 R1.fastq.gz", "0:151 1:151", "A:2048228795;C:1739666332;G:1763496812;T:2041988124;N:773243", 151, 151, null, null, 2048228795, 1739666332, 1763496812, 2041988124, 773243, "SRX4941737", "SRS3985538", "SRA799650", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92922, 0.93046, 0.12988, 0.1333, 0.75657, 0.77684, 0.50439, 0.49684, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49847, "SRR8109598", "SRX4936168", "SRS3980334", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "1h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "1h 1", "1h 1", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "1h-1_R1.fastq.gz 1h-1_R2.fastq.gz", "fastq fastq", 6505465654.0, 21541277.0, "1h 1 R2.fastq.gz", "0:151 1:151", "A:1772064909;C:1473729340;G:1487273483;T:1771747419;N:650503", 151, 151, null, null, 1772064909, 1473729340, 1487273483, 1771747419, 650503, "SRX4936168", "SRS3980334", "SRA798650", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92342, 0.92707, 0.13549, 0.13873, 0.7555, 0.77106, 0.49839, 0.50202, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-25", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49848, "SRR8109308", "SRX4935890", "SRS3980091", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample not treated  replicate #3", "ck 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:not treated  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample not treated  replicate #3", "ck 3", "ck 3", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK-3_R1.fastq.gz CK-3_R2.fastq.gz", "fastq fastq", 6691086632.0, 22155916.0, "CK 3 R2.fastq.gz", "0:151 1:151", "A:1817102254;C:1525946318;G:1537285128;T:1810073033;N:679899", 151, 151, null, null, 1817102254, 1525946318, 1537285128, 1810073033, 679899, "SRX4935890", "SRS3980091", "SRA798632", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93213, 0.93388, 0.10099, 0.10342, 0.75828, 0.77035, 0.49928, 0.49506, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-25", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49849, "SRR8109041", "SRX4935630", "SRS3979958", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample not treated  replicate #2", "ck 2", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:not treated  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample not treated  replicate #2", "ck 2", "ck 2", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK-2_R2.fastq.gz CK-2_R1.fastq.gz", "fastq fastq", 6135368580.0, 20315790.0, "CK 2 R2.fastq.gz", "0:151 1:151", "A:1659190299;C:1402338038;G:1422425283;T:1650808795;N:606165", 151, 151, null, null, 1659190299, 1402338038, 1422425283, 1650808795, 606165, "SRX4935630", "SRS3979958", "SRA798622", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93276, 0.93529, 0.09768, 0.1008, 0.75905, 0.77512, 0.48616, 0.50755, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [64162, "SRR14308451", "SRX10663885", "SRS8758305", "SRP315996", "PRJNA724011", "BDE 47 zebrafish 24hpf 4dpf", "PRJNA724011", "Other", null, null, null, null, null, "C3", null, "strain:AB9|age:24hpf9|dev stage:24hpf9|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AB9", "L9", "L9", "paried end seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP315996", null, null, "C3.raw_1.fastq.gz C3.raw_2.fastq.gz", "fastq fastq", 6301176600.0, 21003922.0, "C3.raw 1.fastq.gz", "0:150 1:150", "A:1665737962;C:1471580978;G:1530541563;T:1633084943;N:231154", 150, 150, null, null, 1665737962, 1471580978, 1530541563, 1633084943, 231154, "SRX10663885", "SRS8758305", "SRA1222808", "Shantou University|Medical Colleg", "Shantou University", 2, 0.93548, 0.93245, 0.07291, 0.07262, 0.76479, 0.76779, 0.47781, 0.4799, 150, 150, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-04-27", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [64985, "SRR14867731", "SRX11185279", "SRS9242606", "SRP324746", "PRJNA739457", "Investigation of mettl4 mediated alterative splicing variation", "GSE178511", "Other", "We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT", null, null, null, "ZEBARFISH WT AB9  Sample 23", "GSM5393117", null, "tissue:ZEBARFISH|genotype:WT|cell line:AB9", "ZEBARFISH WT AB9\u00a0 Sample 23", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10  dm6  sacCer1  GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "ZEBARFISH", null, "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:WT|cell line:AB9", "GSM5393117", "GSM5393117: ZEBARFISH WT AB9  Sample 23; Danio rerio; RNA Seq", "GSM5393117", null, "1", "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5393117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP324746", null, null, "ZEBRAFISH-WT-1_R1_001.fastq.gz ZEBRAFISH-WT-1_R2_001.fastq.gz", "fastq fastq", 8653301400.0, 28844338.0, "GSM5393117 r1", "0:150 1:150", "A:2002938965;C:2340373383;G:2308705634;T:2000755068;N:528350", 150, 150, null, null, 2002938965, 2340373383, 2308705634, 2000755068, 528350, "SRX11185279", "SRS9242606", "SRA1248203", "GEO", "Max Planck Institute for heart and lung research", 2, 0.03799, 0.045, 0.00894, 0.00762, 0.99744, 0.99754, 0.58095, 0.65007, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-06-20", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [64986, "SRR14867730", "SRX11185278", "SRS9242605", "SRP324746", "PRJNA739457", "Investigation of mettl4 mediated alterative splicing variation", "GSE178511", "Other", "We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT", null, null, null, "ZEBARFISH KO AB9  Sample 22", "GSM5393116", null, "tissue:ZEBARFISH|genotype:KO|cell line:AB9", "ZEBARFISH KO AB9\u00a0 Sample 22", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10  dm6  sacCer1  GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "ZEBARFISH", null, "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:KO|cell line:AB9", "GSM5393116", "GSM5393116: ZEBARFISH KO AB9  Sample 22; Danio rerio; RNA Seq", "GSM5393116", null, "1", "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5393116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP324746", null, null, "ZEBRAFISH-KO-1_R1_001.fastq.gz ZEBRAFISH-KO-1_R2_001.fastq.gz", "fastq fastq", 9207894900.0, 30692983.0, "GSM5393116 r1", "0:150 1:150", "A:2082839316;C:2538526142;G:2516073664;T:2069867517;N:588261", 150, 150, null, null, 2082839316, 2538526142, 2516073664, 2069867517, 588261, "SRX11185278", "SRS9242605", "SRA1248203", "GEO", "Max Planck Institute for heart and lung research", 2, 0.0438, 0.05067, 0.00926, 0.00821, 0.99811, 0.99809, 0.5419, 0.60225, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-06-20", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [64987, "SRR14867729", "SRX11185277", "SRS9242604", "SRP324746", "PRJNA739457", "Investigation of mettl4 mediated alterative splicing variation", "GSE178511", "Other", "We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT", null, null, null, "ZEBARFISH WT AB9  Sample 21", "GSM5393115", null, "tissue:ZEBARFISH|genotype:WT|cell line:AB9", "ZEBARFISH WT AB9\u00a0 Sample 21", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10  dm6  sacCer1  GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "ZEBARFISH", null, "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:WT|cell line:AB9", "GSM5393115", "GSM5393115: ZEBARFISH WT AB9  Sample 21; Danio rerio; RNA Seq", "GSM5393115", null, "1", "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5393115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP324746", null, null, "ZEBARFISH-WT-2_R1_001.fastq.gz ZEBARFISH-WT-2_R2_001.fastq.gz", "fastq fastq", 10653778500.0, 35512595.0, "GSM5393115 r1", "0:150 1:150", "A:2472673652;C:2874537502;G:2838089387;T:2467827251;N:650708", 150, 150, null, null, 2472673652, 2874537502, 2838089387, 2467827251, 650708, "SRX11185277", "SRS9242604", "SRA1248203", "GEO", "Max Planck Institute for heart and lung research", 2, 0.03862, 0.04475, 0.0091, 0.00761, 0.99799, 0.99797, 0.57868, 0.65107, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-06-20", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [64988, "SRR14867728", "SRX11185276", "SRS9242603", "SRP324746", "PRJNA739457", "Investigation of mettl4 mediated alterative splicing variation", "GSE178511", "Other", "We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT", null, null, null, "ZEBARFISH KO AB9  Sample 20", "GSM5393114", null, "tissue:ZEBARFISH|genotype:KO|cell line:AB9", "ZEBARFISH KO AB9\u00a0 Sample 20", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to mm8 whole genome using bowtie v0.12.2 with parameters  q  p 4  e 100  y  a  m 10   best   strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10  dm6  sacCer1  GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample", "ZEBARFISH", null, "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:KO|cell line:AB9", "GSM5393114", "GSM5393114: ZEBARFISH KO AB9  Sample 20; Danio rerio; RNA Seq", "GSM5393114", null, "1", "RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM5393114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP324746", null, null, "ZEBARFISH-KO-2_R1_001.fastq.gz ZEBARFISH-KO-2_R2_001.fastq.gz", "fastq fastq", 9242598600.0, 30808662.0, "GSM5393114 r1", "0:150 1:150", "A:2080767915;C:2558275771;G:2525416712;T:2077571589;N:566613", 150, 150, null, null, 2080767915, 2558275771, 2525416712, 2077571589, 566613, "SRX11185276", "SRS9242603", "SRA1248203", "GEO", "Max Planck Institute for heart and lung research", 2, 0.04236, 0.04892, 0.00894, 0.00824, 0.99811, 0.99778, 0.57672, 0.66693, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2021-06-20", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71391, "SRR21563983", "SRX17566322", "SRS15108370", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "10ng/mL TGFB1 treated ZMEL1 Replicate 3", "GSM6579025", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing", "10ng/mL TGFB1 treated ZMEL1 Replicate 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:TGFB1", "GSM6579025", "GSM6579025: 10ng/mL TGFB1 treated ZMEL1 Replicate 3; Danio rerio; RNA Seq", "GSM6579025 r1", "GSM6579025", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN74_R1_001.fastq.gz HN74_R2_001.fastq.gz", "fastq fastq", 10636363800.0, 35454546.0, "GSM6579025 r1", "0:150 1:150", "A:2029842779;C:3291717009;G:3355095939;T:1958873670;N:834403", 150, 150, null, null, 2029842779, 3291717009, 3355095939, 1958873670, 834403, "SRX17566322", "SRS15108370", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93331, 0.94647, 0.18347, 0.19102, 0.85163, 0.86429, 0.71853, 0.75127, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71392, "SRR21563984", "SRX17566321", "SRS15108369", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "10ng/mL TGFB1 treated ZMEL1 Replicate 2", "GSM6579024", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing", "10ng/mL TGFB1 treated ZMEL1 Replicate 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:TGFB1", "GSM6579024", "GSM6579024: 10ng/mL TGFB1 treated ZMEL1 Replicate 2; Danio rerio; RNA Seq", "GSM6579024 r1", "GSM6579024", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN73_R1_001.fastq.gz HN73_R2_001.fastq.gz", "fastq fastq", 8998062900.0, 29993543.0, "GSM6579024 r1", "0:150 1:150", "A:1717609888;C:2782898315;G:2831578316;T:1665301010;N:675371", 150, 150, null, null, 1717609888, 2782898315, 2831578316, 1665301010, 675371, "SRX17566321", "SRS15108369", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93781, 0.94782, 0.184, 0.19138, 0.8449, 0.86014, 0.71335, 0.71676, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71393, "SRR21563985", "SRX17566320", "SRS15108368", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "10ng/mL TGFB1 treated ZMEL1 Replicate 1", "GSM6579023", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing", "10ng/mL TGFB1 treated ZMEL1 Replicate 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:TGFB1", "GSM6579023", "GSM6579023: 10ng/mL TGFB1 treated ZMEL1 Replicate 1; Danio rerio; RNA Seq", "GSM6579023 r1", "GSM6579023", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN72_R1_001.fastq.gz HN72_R2_001.fastq.gz", "fastq fastq", 9469796100.0, 31565987.0, "GSM6579023 r1", "0:150 1:150", "A:1779087329;C:2959081502;G:3015100670;T:1715714055;N:812544", 150, 150, null, null, 1779087329, 2959081502, 3015100670, 1715714055, 812544, "SRX17566320", "SRS15108368", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93963, 0.94978, 0.17963, 0.18558, 0.84691, 0.86032, 0.72223, 0.75653, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71394, "SRR21563986", "SRX17566319", "SRS15108367", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "Vehicle Control treated ZMEL1 Replicate 3", "GSM6579022", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing", "Vehicle Control treated ZMEL1 Replicate 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:Vehicle", "GSM6579022", "GSM6579022: Vehicle Control treated ZMEL1 Replicate 3; Danio rerio; RNA Seq", "GSM6579022 r1", "GSM6579022", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN71_R1_001.fastq.gz HN71_R2_001.fastq.gz", "fastq fastq", 7971184800.0, 26570616.0, "GSM6579022 r1", "0:150 1:150", "A:1508647225;C:2475104436;G:2532882877;T:1453950842;N:599420", 150, 150, null, null, 1508647225, 2475104436, 2532882877, 1453950842, 599420, "SRX17566319", "SRS15108367", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93862, 0.94897, 0.18002, 0.18677, 0.84555, 0.86198, 0.7493, 0.75354, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71395, "SRR21563987", "SRX17566318", "SRS15108366", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "Vehicle Control treated ZMEL1 Replicate 2", "GSM6579021", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing", "Vehicle Control treated ZMEL1 Replicate 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:Vehicle", "GSM6579021", "GSM6579021: Vehicle Control treated ZMEL1 Replicate 2; Danio rerio; RNA Seq", "GSM6579021 r1", "GSM6579021", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN70_R1_001.fastq.gz HN70_R2_001.fastq.gz", "fastq fastq", 11384890800.0, 37949636.0, "GSM6579021 r1", "0:150 1:150", "A:2150820071;C:3536644295;G:3597916072;T:2098730563;N:779799", 150, 150, null, null, 2150820071, 3536644295, 3597916072, 2098730563, 779799, "SRX17566318", "SRS15108366", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93899, 0.94702, 0.17416, 0.18046, 0.84147, 0.85433, 0.75163, 0.66088, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [71396, "SRR21563988", "SRX17566317", "SRS15108365", "SRP397072", "PRJNA880540", "A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq  ZMEL]", "GSE213328", "Transcriptome Analysis", "Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response  while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler  SATB2  which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/  TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours  then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate.", "parent bioproject:PRJNA880593", null, null, "Vehicle Control treated ZMEL1 Replicate 1", "GSM6579020", null, "tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing", "Vehicle Control treated ZMEL1 Replicate 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file", "ZMEL1 Cells", "Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", "ZMEL1 were grown in filter sterilized DMEM  10% FBS  1% PenStrep  1% Glutamine at 28\u00b0C", "cell line:ZMEL1 Cells|treatment:Vehicle", "GSM6579020", "GSM6579020: Vehicle Control treated ZMEL1 Replicate 1; Danio rerio; RNA Seq", "GSM6579020 r1", "GSM6579020", "1", "RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented  reverse transcribed  and library prepped NEB #E7530  NEB #E7335.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP397072", null, null, "HN69_R1_001.fastq.gz HN69_R2_001.fastq.gz", "fastq fastq", 7923946200.0, 26413154.0, "GSM6579020 r1", "0:150 1:150", "A:1526034388;C:2436567275;G:2481233024;T:1479490022;N:621491", 150, 150, null, null, 1526034388, 2436567275, 2481233024, 1479490022, 621491, "SRX17566317", "SRS15108365", null, null, "Oncology/Hematology, Boston Children's Hospital", 2, 0.93823, 0.94638, 0.18016, 0.18529, 0.83481, 0.84928, 0.71588, 0.74024, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "sc_generic", "bulk", "bulk", null, "United States", "2022-09-14", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [74024, "SRR23340934", "SRX19282969", "SRS16684633", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "ERM H4", "GSM7025527", null, "tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing", "ERM H4", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:Control", "GSM7025527", "GSM7025527: ERM H4; Danio rerio; RNA Seq", "GSM7025527 r1", "GSM7025527", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "ERM4_1.fq.gz ERM4_2.fq.gz", "fastq fastq", 9381788700.0, 31272629.0, "GSM7025527 r1", "0:150 1:150", "A:2457973598;C:2250509192;G:2251360794;T:2421836284;N:108832", 150, 150, null, null, 2457973598, 2250509192, 2251360794, 2421836284, 108832, "SRX19282969", "SRS16684633", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96496, 0.96678, 0.09461, 0.09508, 0.68962, 0.68911, 0.48319, 0.48037, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74025, "SRR23340935", "SRX19282968", "SRS16684632", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "ERM H3", "GSM7025526", null, "tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing", "ERM H3", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:Control", "GSM7025526", "GSM7025526: ERM H3; Danio rerio; RNA Seq", "GSM7025526 r1", "GSM7025526", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "ERM3_1.fq.gz ERM3_2.fq.gz", "fastq fastq", 6848962800.0, 22829876.0, "GSM7025526 r1", "0:150 1:150", "A:1832102949;C:1607836088;G:1604618541;T:1804326255;N:78967", 150, 150, null, null, 1832102949, 1607836088, 1604618541, 1804326255, 78967, "SRX19282968", "SRS16684632", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96236, 0.96298, 0.11466, 0.11505, 0.67669, 0.6771, 0.46065, 0.47797, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74026, "SRR23340936", "SRX19282967", "SRS16684631", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "ERM H2", "GSM7025525", null, "tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing", "ERM H2", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:Control", "GSM7025525", "GSM7025525: ERM H2; Danio rerio; RNA Seq", "GSM7025525 r1", "GSM7025525", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "ERM2_1.fq.gz ERM2_2.fq.gz", "fastq fastq", 8055333600.0, 26851112.0, "GSM7025525 r1", "0:150 1:150", "A:2174113541;C:1873627794;G:1868962308;T:2138528112;N:101845", 150, 150, null, null, 2174113541, 1873627794, 1868962308, 2138528112, 101845, "SRX19282967", "SRS16684631", "SRA1723725", "University of Florida", "University of Florida", 2, 0.95895, 0.96097, 0.11791, 0.11772, 0.68434, 0.6832, 0.4604, 0.46478, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74027, "SRR23340937", "SRX19282966", "SRS16684630", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "ERM H1", "GSM7025524", null, "tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing", "ERM H1", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:Control", "GSM7025524", "GSM7025524: ERM H1; Danio rerio; RNA Seq", "GSM7025524 r1", "GSM7025524", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "ERM1_1.fq.gz ERM1_2.fq.gz", "fastq fastq", 8012264100.0, 26707547.0, "GSM7025524 r1", "0:150 1:150", "A:2136077211;C:1883152732;G:1885576694;T:2107363535;N:93928", 150, 150, null, null, 2136077211, 1883152732, 1885576694, 2107363535, 93928, "SRX19282966", "SRS16684630", "SRA1723725", "University of Florida", "University of Florida", 2, 0.95988, 0.96103, 0.12399, 0.12366, 0.67568, 0.67639, 0.47545, 0.47475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74028, "SRR23340938", "SRX19282965", "SRS16684629", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS L5", "GSM7025523", null, "tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing", "AVS L5", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS low dose", "GSM7025523", "GSM7025523: AVS L5; Danio rerio; RNA Seq", "GSM7025523 r1", "GSM7025523", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_L5_2.fq.gz AVS_L5_1.fq.gz", "fastq fastq", 5394091800.0, 17980306.0, "GSM7025523 r1", "0:150 1:150", "A:1448537185;C:1263316442;G:1256083044;T:1426126345;N:28784", 150, 150, null, null, 1448537185, 1263316442, 1256083044, 1426126345, 28784, "SRX19282965", "SRS16684629", "SRA1723725", "University of Florida", "University of Florida", 2, 0.95782, 0.95728, 0.11549, 0.11583, 0.67077, 0.6704, 0.48026, 0.47831, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74029, "SRR23340943", "SRX19282964", "SRS16684628", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS L4", "GSM7025522", null, "tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing", "AVS L4", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS low dose", "GSM7025522", "GSM7025522: AVS L4; Danio rerio; RNA Seq", "GSM7025522 r1", "GSM7025522", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_L4_1.fq.gz AVS_L4_2.fq.gz", "fastq fastq", 6218239800.0, 20727466.0, "GSM7025522 r1", "0:150 1:150", "A:1670735362;C:1455517205;G:1450471834;T:1641444300;N:71099", 150, 150, null, null, 1670735362, 1455517205, 1450471834, 1641444300, 71099, "SRX19282964", "SRS16684628", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96126, 0.96248, 0.13417, 0.13352, 0.67349, 0.67367, 0.47078, 0.47205, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74030, "SRR23340939", "SRX19282963", "SRS16684627", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS L2", "GSM7025521", null, "tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing", "AVS L2", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS low dose", "GSM7025521", "GSM7025521: AVS L2; Danio rerio; RNA Seq", "GSM7025521 r1", "GSM7025521", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_L2_1.fq.gz AVS_L2_2.fq.gz", "fastq fastq", 7843526400.0, 26145088.0, "GSM7025521 r1", "0:150 1:150", "A:2045499665;C:1889002910;G:1889715744;T:2019216443;N:91638", 150, 150, null, null, 2045499665, 1889002910, 1889715744, 2019216443, 91638, "SRX19282963", "SRS16684627", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96621, 0.96656, 0.08667, 0.08617, 0.68189, 0.68193, 0.47856, 0.47892, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74031, "SRR23340942", "SRX19282962", "SRS16684626", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS L1", "GSM7025520", null, "tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing", "AVS L1", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS low dose", "GSM7025520", "GSM7025520: AVS L1; Danio rerio; RNA Seq", "GSM7025520 r1", "GSM7025520", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_L1_1.fq.gz AVS_L1_2.fq.gz", "fastq fastq", 8209836300.0, 27366121.0, "GSM7025520 r1", "0:150 1:150", "A:2129893804;C:1987479891;G:1991913752;T:2100452654;N:96199", 150, 150, null, null, 2129893804, 1987479891, 1991913752, 2100452654, 96199, "SRX19282962", "SRS16684626", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96585, 0.96697, 0.07505, 0.07495, 0.69992, 0.7007, 0.47977, 0.48299, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74032, "SRR23340940", "SRX19282961", "SRS16684625", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS H4", "GSM7025519", null, "tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing", "AVS H4", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS high dose", "GSM7025519", "GSM7025519: AVS H4; Danio rerio; RNA Seq", "GSM7025519 r1", "GSM7025519", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_H4_1.fq.gz AVS_H4_2.fq.gz", "fastq fastq", 7342444200.0, 24474814.0, "GSM7025519 r1", "0:150 1:150", "A:1937996072;C:1753867598;G:1743613654;T:1906882076;N:84800", 150, 150, null, null, 1937996072, 1753867598, 1743613654, 1906882076, 84800, "SRX19282961", "SRS16684625", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96493, 0.95536, 0.09819, 0.097, 0.69891, 0.6994, 0.47856, 0.47909, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74033, "SRR23340941", "SRX19282960", "SRS16684624", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS H3", "GSM7025518", null, "tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing", "AVS H3", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS high dose", "GSM7025518", "GSM7025518: AVS H3; Danio rerio; RNA Seq", "GSM7025518 r1", "GSM7025518", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_H3_1.fq.gz AVS_H3_2.fq.gz", "fastq fastq", 6872036400.0, 22906788.0, "GSM7025518 r1", "0:150 1:150", "A:1794391057;C:1653946970;G:1656595947;T:1767022732;N:79694", 150, 150, null, null, 1794391057, 1653946970, 1656595947, 1767022732, 79694, "SRX19282960", "SRS16684624", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96737, 0.96839, 0.086, 0.0867, 0.68917, 0.69012, 0.47371, 0.4749, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74034, "SRR23340944", "SRX19282959", "SRS16684623", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS H2", "GSM7025517", null, "tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing", "AVS H2", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS high dose", "GSM7025517", "GSM7025517: AVS H2; Danio rerio; RNA Seq", "GSM7025517 r1", "GSM7025517", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_H2_1.fq.gz AVS_H2_2.fq.gz", "fastq fastq", 4536909600.0, 15123032.0, "GSM7025517 r1", "0:150 1:150", "A:1198114288;C:1083631001;G:1079014222;T:1176097255;N:52834", 150, 150, null, null, 1198114288, 1083631001, 1079014222, 1176097255, 52834, "SRX19282959", "SRS16684623", "SRA1723725", "University of Florida", "University of Florida", 2, 0.96395, 0.96493, 0.10052, 0.10013, 0.69832, 0.69895, 0.47664, 0.46072, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"], [74035, "SRR23340945", "SRX19282958", "SRS16684622", "SRP420989", "PRJNA931595", "The effects of atorvastatin AVS and afidopyropen on developing zebrafish", "GSE224522", "Transcriptome Analysis", "For RNA seq experiments  20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf  fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments:  ERM  [100 ng/L AVS or 1 \u00b5g/L AVS] or [100 ng/L or  1 \u00b5g/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.", null, null, null, "AVS H1", "GSM7025516", null, "tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing", "AVS H1", "Raw data raw reads of FASTQ format were firstly processed through fastp. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene  including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count  fpkm  log2 fold change  p value Supplementary files format and content: Afid vs ERM excel files containing read count  fpkm  log2 fold change  p value", "larvae", null, "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "cell line:whole larvae|treatment:AVS high dose", "GSM7025516", "GSM7025516: AVS H1; Danio rerio; RNA Seq", "GSM7025516 r1", "GSM7025516", "1", "Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit\u00ae 2.0 Fluorometer ThermoFisher/Invitrogen  Grand Island  NY  and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies  Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library\" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs  catalog # E7490. RNA library construction was then performed with the NEBNext\u00ae Ultra\u2122 II Directional RNA Library Prep Kit for Illumina\u00ae New England Biolabs  catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc.  CA  U.S.A. Sequencing was performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420989", null, "loader:fastq load.py", "AVS_H1_1.fq.gz AVS_H1_2.fq.gz", "fastq fastq", 5335430400.0, 17784768.0, "GSM7025516 r1", "0:150 1:150", "A:1447500546;C:1236760123;G:1231786894;T:1419321777;N:61060", 150, 150, null, null, 1447500546, 1236760123, 1231786894, 1419321777, 61060, "SRX19282958", "SRS16684622", "SRA1723725", "University of Florida", "University of Florida", 2, 0.95905, 0.95961, 0.13292, 0.13233, 0.67917, 0.68069, 0.48434, 0.48346, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2023-02-04", "Larval", "Larval", "Cell Line", "Cell Line"]], "truncated": false, "filtered_table_rows_count": 107, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.platform\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "ILLUMINA", "p2": "Cell Line"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 107, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 105, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "cDNA", "label": "cDNA", "count": 53, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_selection=cDNA", "selected": false}, {"value": "PCR", "label": "PCR", "count": 35, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_selection=PCR", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&experiment.library_selection=RANDOM+PCR", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 107, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 107, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&tissue_curation=Cell+Line", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 35, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&devstage_curation_coarse=Larval", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 63, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&devstage_curation=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 35, "toggle_url": 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"bulk", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&technology=bulk", "selected": false}, {"value": "10x", "label": "10x", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&technology=10x", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "74035", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.platform=ILLUMINA&tissue_curation=Cell+Line&_next=74035", "private": false, "allow_execute_sql": true, "query_ms": 120.77084499469493}