{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", tissue_curation = \"Cell Line\" and tissue_curation_coarse = \"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. 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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. 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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"], [32865, "SRR29488925", "SRX24999628", "SRS21700588", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "DKO5", "GSM8343040", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing", "DKO5", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO", "GSM8343040", "GSM8343040: DKO5; Danio rerio; RNA Seq", "GSM8343040 r1", "GSM8343040", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "DKO5_1.fq.gz DKO5_2.fq.gz", "fastq fastq", 4813408600.0, 24067043.0, "GSM8343040 r1", "0:100 1:100", "A:1302917202;C:1105312585;G:1123058369;T:1282120444;N:0", 100, 100, null, null, 1302917202, 1105312585, 1123058369, 1282120444, 0, "SRX24999628", "SRS21700588", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32866, "SRR29488926", "SRX24999627", "SRS21700587", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "DKO4", "GSM8343039", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing", "DKO4", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO", "GSM8343039", "GSM8343039: DKO4; Danio rerio; RNA Seq", "GSM8343039 r1", "GSM8343039", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "DKO4_1.fq.gz DKO4_2.fq.gz", "fastq fastq", 4825860200.0, 24129301.0, "GSM8343039 r1", "0:100 1:100", "A:1303584214;C:1108617528;G:1131675283;T:1281983175;N:0", 100, 100, null, null, 1303584214, 1108617528, 1131675283, 1281983175, 0, "SRX24999627", "SRS21700587", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32867, "SRR29488927", "SRX24999626", "SRS21700586", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "DKO3", "GSM8343038", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing", "DKO3", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO", "GSM8343038", "GSM8343038: DKO3; Danio rerio; RNA Seq", "GSM8343038 r1", "GSM8343038", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "DKO3_1.fq.gz DKO3_2.fq.gz", "fastq fastq", 4806754400.0, 24033772.0, "GSM8343038 r1", "0:100 1:100", "A:1289902978;C:1113397086;G:1131727783;T:1271726553;N:0", 100, 100, null, null, 1289902978, 1113397086, 1131727783, 1271726553, 0, "SRX24999626", "SRS21700586", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32868, "SRR29488928", "SRX24999625", "SRS21700585", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "DKO2", "GSM8343037", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing", "DKO2", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO", "GSM8343037", "GSM8343037: DKO2; Danio rerio; RNA Seq", "GSM8343037 r1", "GSM8343037", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "DKO2_1.fq.gz DKO2_2.fq.gz", "fastq fastq", 4805757800.0, 24028789.0, "GSM8343037 r1", "0:100 1:100", "A:1299804990;C:1103101159;G:1124220106;T:1278631545;N:0", 100, 100, null, null, 1299804990, 1103101159, 1124220106, 1278631545, 0, "SRX24999625", "SRS21700585", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32869, "SRR29488929", "SRX24999624", "SRS21700584", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "DKO1", "GSM8343036", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO|geo loc name:missing|collection date:missing", "DKO1", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:DKO", "GSM8343036", "GSM8343036: DKO1; Danio rerio; RNA Seq", "GSM8343036 r1", "GSM8343036", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "DKO1_1.fq.gz DKO1_2.fq.gz", "fastq fastq", 4819172400.0, 24095862.0, "GSM8343036 r1", "0:100 1:100", "A:1296017748;C:1112321357;G:1133115185;T:1277718110;N:0", 100, 100, null, null, 1296017748, 1112321357, 1133115185, 1277718110, 0, "SRX24999624", "SRS21700584", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32870, "SRR29488930", "SRX24999623", "SRS21700583", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "GLO1KO5", "GSM8343035", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing", "GLO1KO5", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO", "GSM8343035", "GSM8343035: GLO1KO5; Danio rerio; RNA Seq", "GSM8343035 r1", "GSM8343035", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "GLO1KO5_1.fq.gz GLO1KO5_2.fq.gz", "fastq fastq", 4813614800.0, 24068074.0, "GSM8343035 r1", "0:100 1:100", "A:1289774342;C:1116099072;G:1136080400;T:1271660986;N:0", 100, 100, null, null, 1289774342, 1116099072, 1136080400, 1271660986, 0, "SRX24999623", "SRS21700583", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32871, "SRR29488931", "SRX24999622", "SRS21700582", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "GLO1KO4", "GSM8343034", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing", "GLO1KO4", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO", "GSM8343034", "GSM8343034: GLO1KO4; Danio rerio; RNA Seq", "GSM8343034 r1", "GSM8343034", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "GLO1KO4_1.fq.gz GLO1KO4_2.fq.gz", "fastq fastq", 4805954200.0, 24029771.0, "GSM8343034 r1", "0:100 1:100", "A:1288997011;C:1113616764;G:1132409574;T:1270930851;N:0", 100, 100, null, null, 1288997011, 1113616764, 1132409574, 1270930851, 0, "SRX24999622", "SRS21700582", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32872, "SRR29488932", "SRX24999621", "SRS21700581", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "GLO1KO3", "GSM8343033", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing", "GLO1KO3", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO", "GSM8343033", "GSM8343033: GLO1KO3; Danio rerio; RNA Seq", "GSM8343033 r1", "GSM8343033", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "GLO1KO3_1.fq.gz GLO1KO3_2.fq.gz", "fastq fastq", 4817965600.0, 24089828.0, "GSM8343033 r1", "0:100 1:100", "A:1290593290;C:1118086028;G:1134064137;T:1275222145;N:0", 100, 100, null, null, 1290593290, 1118086028, 1134064137, 1275222145, 0, "SRX24999621", "SRS21700581", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32873, "SRR29488933", "SRX24999620", "SRS21700580", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "GLO1KO2", "GSM8343032", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing", "GLO1KO2", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO", "GSM8343032", "GSM8343032: GLO1KO2; Danio rerio; RNA Seq", "GSM8343032 r1", "GSM8343032", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "GLO1KO2_1.fq.gz GLO1KO2_2.fq.gz", "fastq fastq", 4805999000.0, 24029995.0, "GSM8343032 r1", "0:100 1:100", "A:1293609489;C:1109265811;G:1128786421;T:1274337279;N:0", 100, 100, null, null, 1293609489, 1109265811, 1128786421, 1274337279, 0, "SRX24999620", "SRS21700580", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32874, "SRR29488934", "SRX24999619", "SRS21700579", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "GLO1KO1", "GSM8343031", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO|geo loc name:missing|collection date:missing", "GLO1KO1", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:GLO1KO", "GSM8343031", "GSM8343031: GLO1KO1; Danio rerio; RNA Seq", "GSM8343031 r1", "GSM8343031", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "GLO1KO1_1.fq.gz GLO1KO1_2.fq.gz", "fastq fastq", 4806768400.0, 24033842.0, "GSM8343031 r1", "0:100 1:100", "A:1286467027;C:1115478546;G:1135313631;T:1269509196;N:0", 100, 100, null, null, 1286467027, 1115478546, 1135313631, 1269509196, 0, "SRX24999619", "SRS21700579", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32875, "SRR29488935", "SRX24999618", "SRS21700578", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "ALDH3A1KO5", "GSM8343030", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing", "ALDH3A1KO5", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO", "GSM8343030", "GSM8343030: ALDH3A1KO5; Danio rerio; RNA Seq", "GSM8343030 r1", "GSM8343030", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "ALDH3A1KO5_1.fq.gz ALDH3A1KO5_2.fq.gz", "fastq fastq", 4811331000.0, 24056655.0, "GSM8343030 r1", "0:100 1:100", "A:1314568654;C:1091419677;G:1111494171;T:1293848498;N:0", 100, 100, null, null, 1314568654, 1091419677, 1111494171, 1293848498, 0, "SRX24999618", "SRS21700578", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32876, "SRR29488936", "SRX24999617", "SRS21700577", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "ALDH3A1KO4", "GSM8343029", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing", "ALDH3A1KO4", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO", "GSM8343029", "GSM8343029: ALDH3A1KO4; Danio rerio; RNA Seq", "GSM8343029 r1", "GSM8343029", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "ALDH3A1KO4_1.fq.gz ALDH3A1KO4_2.fq.gz", "fastq fastq", 4816993800.0, 24084969.0, "GSM8343029 r1", "0:100 1:100", "A:1320840277;C:1087361823;G:1108886472;T:1299905228;N:0", 100, 100, null, null, 1320840277, 1087361823, 1108886472, 1299905228, 0, "SRX24999617", "SRS21700577", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32877, "SRR29488937", "SRX24999616", "SRS21700576", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "ALDH3A1KO3", "GSM8343028", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing", "ALDH3A1KO3", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO", "GSM8343028", "GSM8343028: ALDH3A1KO3; Danio rerio; RNA Seq", "GSM8343028 r1", "GSM8343028", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "ALDH3A1KO3_1.fq.gz ALDH3A1KO3_2.fq.gz", "fastq fastq", 4828261200.0, 24141306.0, "GSM8343028 r1", "0:100 1:100", "A:1325980327;C:1088988247;G:1107987702;T:1305304924;N:0", 100, 100, null, null, 1325980327, 1088988247, 1107987702, 1305304924, 0, "SRX24999616", "SRS21700576", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32878, "SRR29488938", "SRX24999615", "SRS21700575", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "ALDH3A1KO2", "GSM8343027", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing", "ALDH3A1KO2", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO", "GSM8343027", "GSM8343027: ALDH3A1KO2; Danio rerio; RNA Seq", "GSM8343027 r1", "GSM8343027", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "ALDH3A1KO2_1.fq.gz ALDH3A1KO2_2.fq.gz", "fastq fastq", 4806790400.0, 24033952.0, "GSM8343027 r1", "0:100 1:100", "A:1296924744;C:1110667292;G:1117161162;T:1282037202;N:0", 100, 100, null, null, 1296924744, 1110667292, 1117161162, 1282037202, 0, "SRX24999615", "SRS21700575", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32879, "SRR29488939", "SRX24999614", "SRS21700574", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "ALDH3A1KO1", "GSM8343026", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO|geo loc name:missing|collection date:missing", "ALDH3A1KO1", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:ALDH3A1KO", "GSM8343026", "GSM8343026: ALDH3A1KO1; Danio rerio; RNA Seq", "GSM8343026 r1", "GSM8343026", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "ALDH3A1KO1_1.fq.gz ALDH3A1KO1_2.fq.gz", "fastq fastq", 4801013600.0, 24005068.0, "GSM8343026 r1", "0:100 1:100", "A:1307355551;C:1094613295;G:1111765622;T:1287279132;N:0", 100, 100, null, null, 1307355551, 1094613295, 1111765622, 1287279132, 0, "SRX24999614", "SRS21700574", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32880, "SRR29488940", "SRX24999613", "SRS21700573", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "WT5", "GSM8343025", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing", "WT5", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT", "GSM8343025", "GSM8343025: WT5; Danio rerio; RNA Seq", "GSM8343025 r1", "GSM8343025", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "WT5_1.fq.gz WT5_2.fq.gz", "fastq fastq", 4820580400.0, 24102902.0, "GSM8343025 r1", "0:100 1:100", "A:1288306977;C:1120287477;G:1138943028;T:1273042918;N:0", 100, 100, null, null, 1288306977, 1120287477, 1138943028, 1273042918, 0, "SRX24999613", "SRS21700573", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32881, "SRR29488941", "SRX24999612", "SRS21700572", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "WT4", "GSM8343024", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing", "WT4", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT", "GSM8343024", "GSM8343024: WT4; Danio rerio; RNA Seq", "GSM8343024 r1", "GSM8343024", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "WT4_1.fq.gz WT4_2.fq.gz", "fastq fastq", 4821144600.0, 24105723.0, "GSM8343024 r1", "0:100 1:100", "A:1275218149;C:1133748961;G:1151831603;T:1260345887;N:0", 100, 100, null, null, 1275218149, 1133748961, 1151831603, 1260345887, 0, "SRX24999612", "SRS21700572", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32882, "SRR29488942", "SRX24999611", "SRS21700571", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "WT3", "GSM8343023", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing", "WT3", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT", "GSM8343023", "GSM8343023: WT3; Danio rerio; RNA Seq", "GSM8343023 r1", "GSM8343023", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 4826072600.0, 24130363.0, "GSM8343023 r1", "0:100 1:100", "A:1278424901;C:1132200743;G:1150406212;T:1265040744;N:0", 100, 100, null, null, 1278424901, 1132200743, 1150406212, 1265040744, 0, "SRX24999611", "SRS21700571", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32883, "SRR29488943", "SRX24999610", "SRS21700570", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "WT2", "GSM8343022", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing", "WT2", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT", "GSM8343022", "GSM8343022: WT2; Danio rerio; RNA Seq", "GSM8343022 r1", "GSM8343022", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 4801181000.0, 24005905.0, "GSM8343022 r1", "0:100 1:100", "A:1271169177;C:1127438892;G:1145437659;T:1257135272;N:0", 100, 100, null, null, 1271169177, 1127438892, 1145437659, 1257135272, 0, "SRX24999610", "SRS21700570", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "Larval", "Larval", "Cell Line", "Cell Line"], [32884, "SRR29488944", "SRX24999609", "SRS21700569", "SRP515253", "PRJNA1126644", "Elevated MG H1 in glo1 / aldh3a1 / zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity", "GSE270442", "Transcriptome Analysis", "Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites leading to increased modification of proteins DNA and lipids thereby contributing to cellular and tissue dysfunction in diabetes diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels which partially act as compensatory mechanism. Excess 4 HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish. glo1 / aldh3a1 / zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG H1 and decreased proteasomal chymotrypsin like activity which could be rescued by the MG H1 scavenger L carnosine and proteasome activator Betulinic acid treatments. In adult glo1 / aldh3a1 / zebrafish impaired glucose metabolism angiogenic retina vasculature and thickened GBM were observed. Thus our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG H1 possibly through reduced proteasome activity. Overall design: glo1 / aldh3a1 / zebrafish were generated using CRISPR/Cas9 technology. Multiple experiments are performed regarding vasculature alterations glucose homeostasis transcriptome and metabolomics in Tgfli1:EGFP zebrafish.", null, null, null, "WT1", "GSM8343021", null, "source name:larvae|tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT|geo loc name:missing|collection date:missing", "WT1", "Raw sequence data with adapter sequences or low quality sequences was filtered. Filtered reads were aligned to the Zebrafish reference genome GRCz11 Raw counts levels were quantified using FeatureCounts v2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each sample.", "larvae", null, "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "tissue:larvae|cell line:Tgfli1:EGFP|cell type:larvae|genotype:WT", "GSM8343021", "GSM8343021: WT1; Danio rerio; RNA Seq", "GSM8343021 r1", "GSM8343021", "1", "Total RNA was extracted using RNeasy Mini KitQIAGEN 3ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA seq were prepared using DNBSEQ Eukaryotic Strand specific mRNA library.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP515253", null, null, "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 4802502800.0, 24012514.0, "GSM8343021 r1", "0:100 1:100", "A:1263416018;C:1135581393;G:1152700487;T:1250804902;N:0", 100, 100, null, null, 1263416018, 1135581393, 1152700487, 1250804902, 0, "SRX24999609", "SRS21700569", "SRA1904686", "ECAS", "ECAS", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-06-21", "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. 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, "Control3_R1.fastq.gz Control3_R2.fastq.gz", "fastq fastq", 8332352744.0, 27590572.0, "Control3 R1.fastq.gz", "0:151 1:151", "A:2202584495;C:1949417777;G:1998200355;T:2181578177;N:571940", 151, 151, null, null, 2202584495, 1949417777, 1998200355, 2181578177, 571940, "SRX26409985", "SRS22929898", "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"], [33988, "SRR31022899", "SRX26409984", "SRS22929897", "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: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. 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, "Control2_R1.fastq.gz Control2_R2.fastq.gz", "fastq fastq", 6938613986.0, 22975543.0, "Control2 R1.fastq.gz", "0:151 1:151", "A:1833222889;C:1624373992;G:1667764740;T:1812783827;N:468538", 151, 151, null, null, 1833222889, 1624373992, 1667764740, 1812783827, 468538, "SRX26409984", "SRS22929897", "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"], [33989, "SRR31022900", "SRX26409983", "SRS22929895", "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: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. 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, "Control1_R1.fastq.gz Control1_R2.fastq.gz", "fastq fastq", 6383504766.0, 21137433.0, "Control1 R1.fastq.gz", "0:151 1:151", "A:1696959129;C:1488903810;G:1519707762;T:1677504326;N:429739", 151, 151, null, null, 1696959129, 1488903810, 1519707762, 1677504326, 429739, "SRX26409983", "SRS22929895", "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"], [34557, "SRR32105502", "SRX27451095", "SRS23877593", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SC2", "SC2", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SC2", "SC2", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301599--SC2.R1.raw.fastq.gz L1EHE2301599--SC2.R2.raw.fastq.gz", "fastq fastq", 12846566600.0, 42538300.0, "L1EHE2301599 SC2.R1.raw.fastq.gz", "0:151 1:151", "A:3482255367;C:2921391563;G:2987736885;T:3455132712;N:50073", 151, 151, null, null, 3482255367, 2921391563, 2987736885, 3455132712, 50073, "SRX27451095", "SRS23877593", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34558, "SRR32105503", "SRX27451094", "SRS23877596", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SC1", "SC1", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SC1", "SC1", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301598--SC1.R1.raw.fastq.gz L1EHE2301598--SC1.R2.raw.fastq.gz", "fastq fastq", 11231331982.0, 37189841.0, "L1EHE2301598 SC1.R1.raw.fastq.gz", "0:151 1:151", "A:3065685647;C:2524957941;G:2595543794;T:3045100764;N:43836", 151, 151, null, null, 3065685647, 2524957941, 2595543794, 3045100764, 43836, "SRX27451094", "SRS23877596", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34573, "SRR32105518", "SRX27451079", "SRS23877577", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SK4", "SK4", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:16|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SK4", "SK4", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301609--SK4.R1.raw.fastq.gz L1EHE2301609--SK4.R2.raw.fastq.gz", "fastq fastq", 12103764380.0, 40078690.0, "L1EHE2301609 SK4.R1.raw.fastq.gz", "0:151 1:151", "A:3257453744;C:2780396394;G:2833143851;T:3232723098;N:47293", 151, 151, null, null, 3257453744, 2780396394, 2833143851, 3232723098, 47293, "SRX27451079", "SRS23877577", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34574, "SRR32105519", "SRX27451078", "SRS23877576", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SK3", "SK3", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:15|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SK3", "SK3", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301608--SK3.R1.raw.fastq.gz L1EHE2301608--SK3.R2.raw.fastq.gz", "fastq fastq", 13563244914.0, 44911407.0, "L1EHE2301608 SK3.R1.raw.fastq.gz", "0:151 1:151", "A:3628034105;C:3137333406;G:3198471155;T:3599351549;N:54699", 151, 151, null, null, 3628034105, 3137333406, 3198471155, 3599351549, 54699, "SRX27451078", "SRS23877576", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34575, "SRR32105520", "SRX27451077", "SRS23877575", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SK2", "SK2", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:14|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SK2", "SK2", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301607--SK2.R1.raw.fastq.gz L1EHE2301607--SK2.R2.raw.fastq.gz", "fastq fastq", 13308976014.0, 44069457.0, "L1EHE2301607 SK2.R1.raw.fastq.gz", "0:151 1:151", "A:3569709366;C:3066880930;G:3123966592;T:3548366304;N:52822", 151, 151, null, null, 3569709366, 3066880930, 3123966592, 3548366304, 52822, "SRX27451077", "SRS23877575", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34576, "SRR32105521", "SRX27451076", "SRS23877581", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SK1", "SK1", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:13|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SK1", "SK1", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301606--SK1.R1.raw.fastq.gz L1EHE2301606--SK1.R2.raw.fastq.gz", "fastq fastq", 13251027348.0, 43877574.0, "L1EHE2301606 SK1.R1.raw.fastq.gz", "0:151 1:151", "A:3562385928;C:3046618953;G:3101399402;T:3540570730;N:52335", 151, 151, null, null, 3562385928, 3046618953, 3101399402, 3540570730, 52335, "SRX27451076", "SRS23877581", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34577, "SRR32105522", "SRX27451075", "SRS23877579", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SC4", "SC4", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SC4", "SC4", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301601--SC4.R1.raw.fastq.gz L1EHE2301601--SC4.R2.raw.fastq.gz", "fastq fastq", 12694824888.0, 42035844.0, "L1EHE2301601 SC4.R1.raw.fastq.gz", "0:151 1:151", "A:3435956769;C:2884050436;G:2964456274;T:3410311062;N:50347", 151, 151, null, null, 3435956769, 2884050436, 2964456274, 3410311062, 50347, "SRX27451075", "SRS23877579", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [34578, "SRR32105523", "SRX27451074", "SRS23877578", "SRP559581", "PRJNA1214993", "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "PRJNA1214993", "Other", "New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.", null, null, null, "SC3", "SC3", null, "breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental toxicity of new psychoactive substance esketamine to zebrafish", "SC3", "SC3", "cell", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP559581", null, null, "L1EHE2301600--SC3.R1.raw.fastq.gz L1EHE2301600--SC3.R2.raw.fastq.gz", "fastq fastq", 12586532218.0, 41677259.0, "L1EHE2301600 SC3.R1.raw.fastq.gz", "0:151 1:151", "A:3422332578;C:2845378360;G:2913592547;T:3405179722;N:49011", 151, 151, null, null, 3422332578, 2845378360, 2913592547, 3405179722, 49011, "SRX27451074", "SRS23877578", "SRA2059104", "South China Normal University|School of Environment", "South China Normal University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-24", "Pharyngula", "Embryo", "Cell Line", "Cell Line"], [36007, "SRR33398626", "SRX28641175", "SRS24911532", "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 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 21|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 212|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", "Ca3", "Ca3", "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-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. 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, "12h2_clean_R1.fq.gz 12h2_clean_R2.fq.gz", "fastq fastq", 5637564766.0, 18667433.0, "12h2 clean R1.fq.gz", "0:151 1:151", "A:1484457309;C:1319928521;G:1331480348;T:1498547286;N:3151302", 151, 151, null, null, 1484457309, 1319928521, 1331480348, 1498547286, 3151302, "SRX5762615", "SRS4697269", "SRA880316", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93974, 0.93913, 0.09518, 0.09588, 0.74982, 0.75331, 0.49858, 0.49712, 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"], [49819, "SRR8983316", "SRX5762614", "SRS4697268", "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 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", "12h 4", "12h 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, "12h1_clean_R2.fq.gz 12h1_clean_R1.fq.gz", "fastq fastq", 5742037438.0, 19013369.0, "12h1 clean R1.fq.gz", "0:151 1:151", "A:1505967171;C:1350499061;G:1361100937;T:1521258216;N:3212053", 151, 151, null, null, 1505967171, 1350499061, 1361100937, 1521258216, 3212053, "SRX5762614", "SRS4697268", "SRA880316", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9408, 0.93974, 0.09145, 0.09155, 0.75146, 0.75501, 0.49821, 0.49267, 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"], [49820, "SRR8983317", "SRX5762613", "SRS4697267", "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 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", "12h 6", "12h 6", "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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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. 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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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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. 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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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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. 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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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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. 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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. 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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. 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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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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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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. 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