{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and tissue_curation = \"Cell Line\"", "rows": [[28458, "SRR26265233", "SRX21974767", "SRS19050630", "SRP464312", "PRJNA1022576", "Danio rerio Raw sequence reads", "PRJNA1022576", "Whole Genome Sequencing", "In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. 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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, "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"], [28470, "SRR26253203", "SRX21963295", "SRS19039869", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 22|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND2", "Small RNA IFND2", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-2.deadaptor.fq.gz", "fastq", 278362309.0, 11056139.0, "IFN4 2.deadaptor.fq.gz", "0:25.18", "A:71944968;C:54562141;G:73333701;T:78511075;N:10424", 25, null, null, null, 71944968, 54562141, 73333701, 78511075, 10424, "SRX21963295", "SRS19039869", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.93133, null, 0.07401, null, 0.96181, null, 0.74558, null, 31, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28471, "SRR26253204", "SRX21963294", "SRS19039868", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 21|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND1", "Small RNA IFND1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-1.deadaptor.fq.gz", "fastq", 289362334.0, 11048590.0, "IFN4 1.deadaptor.fq.gz", "0:26.19", "A:73933649;C:59386039;G:76847534;T:79184583;N:10529", 26, null, null, null, 73933649, 59386039, 76847534, 79184583, 10529, "SRX21963294", "SRS19039868", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91683, null, 0.07099, null, 0.96132, null, 0.64882, null, 25, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28472, "SRR26253205", "SRX21963293", "SRS19039867", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA IFN1 4", null, "strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 20|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA4", "Small RNA IFNA4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-4.deadaptor.fq.gz", "fastq", 270529395.0, 11070360.0, "IFN1 4.deadaptor.fq.gz", "0:24.44", "A:69759888;C:54924667;G:71358091;T:74470720;N:16029", 24, null, null, null, 69759888, 54924667, 71358091, 74470720, 16029, "SRX21963293", "SRS19039867", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.88469, null, 0.06696, null, 0.96664, null, 0.74853, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28473, "SRR26253206", "SRX21963292", "SRS19039866", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 19|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA3", "Small RNA IFNA3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-3.deadaptor.fq.gz", "fastq", 353291957.0, 11740560.0, "IFN1 3.deadaptor.fq.gz", "0:30.09", "A:89026549;C:76490337;G:94719420;T:93036955;N:18696", 30, null, null, null, 89026549, 76490337, 94719420, 93036955, 18696, "SRX21963292", "SRS19039866", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.83151, null, 0.07199, null, 0.96471, null, 0.71641, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28474, "SRR26253207", "SRX21963291", "SRS19039865", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 18|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA2", "Small RNA IFNA2", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-2.deadaptor.fq.gz", "fastq", 257949577.0, 11213774.0, "IFN1 2.deadaptor.fq.gz", "0:23.00", "A:67371681;C:51128621;G:67605590;T:71826657;N:17028", 23, null, null, null, 67371681, 51128621, 67605590, 71826657, 17028, "SRX21963291", "SRS19039865", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91396, null, 0.06536, null, 0.97197, null, 0.76269, null, 23, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28475, "SRR26253208", "SRX21963290", "SRS19039864", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 17|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFNA1", "Small RNA IFNA1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN1-1.deadaptor.fq.gz", "fastq", 329358383.0, 11799176.0, "IFN1 1.deadaptor.fq.gz", "0:27.91", "A:84093681;C:68961271;G:86502739;T:89779605;N:21087", 27, null, null, null, 84093681, 68961271, 86502739, 89779605, 21087, "SRX21963290", "SRS19039864", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.92116, null, 0.07483, null, 0.96796, null, 0.75179, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28476, "SRR26253209", "SRX21963289", "SRS19039863", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 16|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C4", "Small RNA C4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-4.deadaptor.fq.gz", "fastq", 251577736.0, 10951659.0, "Control 4.deadaptor.fq.gz", "0:22.97", "A:65382449;C:50041232;G:66038625;T:70106464;N:8966", 22, null, null, null, 65382449, 50041232, 66038625, 70106464, 8966, "SRX21963289", "SRS19039863", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.89744, null, 0.06821, null, 0.96607, null, 0.63829, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28477, "SRR26253210", "SRX21963288", "SRS19039862", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 15|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C3", "Small RNA C3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-3.deadaptor.fq.gz", "fastq", 252164979.0, 11004167.0, "Control 3.deadaptor.fq.gz", "0:22.92", "A:65850899;C:48466665;G:66708038;T:71130786;N:8591", 22, null, null, null, 65850899, 48466665, 66708038, 71130786, 8591, "SRX21963288", "SRS19039862", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.91567, null, 0.06804, null, 0.96278, null, 0.75579, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28478, "SRR26253211", "SRX21963287", "SRS19039861", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 24|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND4", "Small RNA IFND4", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-4.deadaptor.fq.gz", "fastq", 291708053.0, 11503883.0, "IFN4 4.deadaptor.fq.gz", "0:25.36", "A:74079231;C:61368459;G:76898572;T:79351225;N:10566", 25, null, null, null, 74079231, 61368459, 76898572, 79351225, 10566, "SRX21963287", "SRS19039861", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.88888, null, 0.0633, null, 0.97305, null, 0.74862, null, 23, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28479, "SRR26253212", "SRX21963286", "SRS19039860", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 23|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA IFND3", "Small RNA IFND3", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "IFN4-3.deadaptor.fq.gz", "fastq", 349995495.0, 11885662.0, "IFN4 3.deadaptor.fq.gz", "0:29.45", "A:87443709;C:76373108;G:92741296;T:93425866;N:11516", 29, null, null, null, 87443709, 76373108, 92741296, 93425866, 11516, "SRX21963286", "SRS19039860", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.92619, null, 0.06843, null, 0.9709, null, 0.74977, null, 73, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28480, "SRR26253213", "SRX21963285", "SRS19039859", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 14|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C2", "Small RNA C2", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-2.deadaptor.fq.gz", "fastq", 254163676.0, 10744164.0, "Control 2.deadaptor.fq.gz", "0:23.66", "A:66003417;C:49309846;G:67463940;T:71377644;N:8829", 23, null, null, null, 66003417, 49309846, 67463940, 71377644, 8829, "SRX21963285", "SRS19039859", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.93068, null, 0.06626, null, 0.96441, null, 0.7492, null, 22, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28481, "SRR26253214", "SRX21963284", "SRS19039858", "SRP464138", "PRJNA1022587", "Danio rerio Raw sequence reads", "PRJNA1022587", "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 of the small RNA.", null, null, null, null, "Small RNA 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 13|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNAseq of zebrafish", "Small RNA C1", "Small RNA C1", "small RNA seq of zebrafish", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP464138", null, null, "Control-1.deadaptor.fq.gz", "fastq", 267090429.0, 11027241.0, "Control 1.deadaptor.fq.gz", "0:24.22", "A:70162511;C:50705437;G:69872659;T:76339682;N:10140", 24, null, null, null, 70162511, 50705437, 69872659, 76339682, 10140, "SRX21963284", "SRS19039858", "SRA1724093", "Shanghai Ocean University|College of Fisheries and Life Science", "Shanghai Ocean University", 1, 0.93267, null, 0.07189, null, 0.96735, null, 0.75447, null, 21, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-10-02", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [28985, "SRR26936267", "SRX22630108", "SRS19628590", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 6", "GSM7916507", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "La 6", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916507", "GSM7916507: La 6; Danio rerio; ncRNA Seq", "GSM7916507 r1", "GSM7916507", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X32_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 810705967.0, 27544418.0, "GSM7916507 r1", "0:29.43", "A:141437993;C:173890211;G:258408531;T:236922660;N:46572", 29, null, null, null, 141437993, 173890211, 258408531, 236922660, 46572, "SRX22630108", "SRS19628590", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.86832, null, 0.1884, null, 0.84735, null, 0.64657, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28986, "SRR26936231", "SRX22630107", "SRS19628589", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 5", "GSM7916506", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 5", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916506", "GSM7916506: La 5; Danio rerio; ncRNA Seq", "GSM7916506 r1", "GSM7916506", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X31_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 1237906972.0, 45149037.0, "GSM7916506 r1", "0:27.42", "A:273044213;C:252818121;G:368519115;T:343444331;N:81192", 27, null, null, null, 273044213, 252818121, 368519115, 343444331, 81192, "SRX22630107", "SRS19628589", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.86015, null, 0.25463, null, 0.83798, null, 0.67166, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28987, "SRR26936232", "SRX22630106", "SRS19628588", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 2", "GSM7916505", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 2", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916505", "GSM7916505: Hb 2; Danio rerio; ncRNA Seq", "GSM7916505 r1", "GSM7916505", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X30_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 214730387.0, 7217086.0, "GSM7916505 r1", "0:29.75", "A:42819722;C:48080032;G:67677978;T:56140049;N:12606", 29, null, null, null, 42819722, 48080032, 67677978, 56140049, 12606, "SRX22630106", "SRS19628588", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85212, null, 0.1617, null, 0.86856, null, 0.69163, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28988, "SRR26936233", "SRX22630105", "SRS19628587", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 1", "GSM7916504", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 1", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916504", "GSM7916504: Hb 1; Danio rerio; ncRNA Seq", "GSM7916504 r1", "GSM7916504", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X29_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 595989272.0, 21399963.0, "GSM7916504 r1", "0:27.85", "A:128259525;C:125823294;G:181746588;T:160121380;N:38485", 27, null, null, null, 128259525, 125823294, 181746588, 160121380, 38485, "SRX22630105", "SRS19628587", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85218, null, 0.22941, null, 0.83595, null, 0.6151, null, 30, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28989, "SRR26936234", "SRX22630104", "SRS19628586", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 6", "GSM7916503", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 6", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916503", "GSM7916503: Lb 6; Danio rerio; ncRNA Seq", "GSM7916503 r1", "GSM7916503", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X28_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 969307398.0, 35511411.0, "GSM7916503 r1", "0:27.30", "A:205174189;C:203840471;G:285952255;T:274278193;N:62290", 27, null, null, null, 205174189, 203840471, 285952255, 274278193, 62290, "SRX22630104", "SRS19628586", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85414, null, 0.22608, null, 0.8505, null, 0.62202, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28990, "SRR26936235", "SRX22630103", "SRS19628585", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 6", "GSM7916502", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 6", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916502", "GSM7916502: Ha 6; Danio rerio; ncRNA Seq", "GSM7916502 r1", "GSM7916502", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X27_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 1326612630.0, 47094729.0, "GSM7916502 r1", "0:28.17", "A:303455697;C:273680466;G:382978796;T:366416311;N:81360", 28, null, null, null, 303455697, 273680466, 382978796, 366416311, 81360, "SRX22630103", "SRS19628585", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84786, null, 0.24696, null, 0.82946, null, 0.68975, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28991, "SRR26936236", "SRX22630102", "SRS19628584", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 5", "GSM7916501", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 5", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916501", "GSM7916501: Ha 5; Danio rerio; ncRNA Seq", "GSM7916501 r1", "GSM7916501", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X26_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 471823428.0, 16704799.0, "GSM7916501 r1", "0:28.24", "A:103178860;C:100561292;G:155557190;T:112495106;N:30980", 28, null, null, null, 103178860, 100561292, 155557190, 112495106, 30980, "SRX22630102", "SRS19628584", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.61628, null, 0.14433, null, 0.91275, null, 0.6543, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28992, "SRR26936237", "SRX22630101", "SRS19628583", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 4", "GSM7916500", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 4", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916500", "GSM7916500: La 4; Danio rerio; ncRNA Seq", "GSM7916500 r1", "GSM7916500", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X25_160303_D00294_0224_AC95NJANXX_7.cutadapt.se.19_100.fastq.gz", "fastq", 713371286.0, 25212566.0, "GSM7916500 r1", "0:28.29", "A:155201946;C:151864186;G:207971547;T:198288220;N:45387", 28, null, null, null, 155201946, 151864186, 207971547, 198288220, 45387, "SRX22630101", "SRS19628583", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.8507, null, 0.2078, null, 0.83031, null, 0.62739, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28993, "SRR26936238", "SRX22630100", "SRS19628582", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 5", "GSM7916499", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 5", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916499", "GSM7916499: Hb 5; Danio rerio; ncRNA Seq", "GSM7916499 r1", "GSM7916499", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X24_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 1043060550.0, 35761504.0, "GSM7916499 r1", "0:29.17", "A:217942105;C:216398395;G:316456102;T:292217159;N:46789", 29, null, null, null, 217942105, 216398395, 316456102, 292217159, 46789, "SRX22630100", "SRS19628582", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.82114, null, 0.20881, null, 0.85622, null, 0.68486, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28994, "SRR26936239", "SRX22630099", "SRS19628581", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 4", "GSM7916498", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 4", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916498", "GSM7916498: Hb 4; Danio rerio; ncRNA Seq", "GSM7916498 r1", "GSM7916498", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X23_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 1357956641.0, 47869361.0, "GSM7916498 r1", "0:28.37", "A:293740473;C:276333777;G:404639503;T:383181225;N:61663", 28, null, null, null, 293740473, 276333777, 404639503, 383181225, 61663, "SRX22630099", "SRS19628581", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.79885, null, 0.22306, null, 0.8425, null, 0.6656, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28995, "SRR26936240", "SRX22630098", "SRS19628580", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 5", "GSM7916497", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 5", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916497", "GSM7916497: Lb 5; Danio rerio; ncRNA Seq", "GSM7916497 r1", "GSM7916497", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X22_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 669771811.0, 23848259.0, "GSM7916497 r1", "0:28.08", "A:132916986;C:135594797;G:198730347;T:202498953;N:30728", 28, null, null, null, 132916986, 135594797, 198730347, 202498953, 30728, "SRX22630098", "SRS19628580", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.80999, null, 0.24188, null, 0.84658, null, 0.68339, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28996, "SRR26936241", "SRX22630097", "SRS19628579", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 4", "GSM7916496", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 4", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916496", "GSM7916496: Ha 4; Danio rerio; ncRNA Seq", "GSM7916496 r1", "GSM7916496", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X21_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 853803123.0, 28538725.0, "GSM7916496 r1", "0:29.92", "A:158220512;C:186146914;G:264519321;T:244878221;N:38155", 29, null, null, null, 158220512, 186146914, 264519321, 244878221, 38155, "SRX22630097", "SRS19628579", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.828, null, 0.18458, null, 0.85851, null, 0.6483, null, 32, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28997, "SRR26936242", "SRX22630096", "SRS19628578", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 3", "GSM7916495", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 3", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916495", "GSM7916495: Ha 3; Danio rerio; ncRNA Seq", "GSM7916495 r1", "GSM7916495", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X20_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 629106097.0, 21383957.0, "GSM7916495 r1", "0:29.42", "A:117216944;C:131994022;G:192623524;T:187243523;N:28084", 29, null, null, null, 117216944, 131994022, 192623524, 187243523, 28084, "SRX22630096", "SRS19628578", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.8166, null, 0.20457, null, 0.84112, null, 0.65357, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28998, "SRR26936243", "SRX22630095", "SRS19628577", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 1", "GSM7916494", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 1", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916494", "GSM7916494: La 1; Danio rerio; ncRNA Seq", "GSM7916494 r1", "GSM7916494", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X19_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 21178378.0, 739280.0, "GSM7916494 r1", "0:28.65", "A:4323144;C:4478932;G:6303136;T:6072190;N:976", 28, null, null, null, 4323144, 4478932, 6303136, 6072190, 976, "SRX22630095", "SRS19628577", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85277, null, 0.21158, null, 0.87434, null, 0.62601, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [28999, "SRR26936244", "SRX22630094", "SRS19628576", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 4", "GSM7916493", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 4", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916493", "GSM7916493: Lb 4; Danio rerio; ncRNA Seq", "GSM7916493 r1", "GSM7916493", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X18_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 959247745.0, 33043430.0, "GSM7916493 r1", "0:29.03", "A:225208425;C:212535680;G:284062577;T:237397072;N:43991", 29, null, null, null, 225208425, 212535680, 284062577, 237397072, 43991, "SRX22630094", "SRS19628576", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.82232, null, 0.22592, null, 0.87073, null, 0.6135, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29000, "SRR26936245", "SRX22630093", "SRS19628575", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 3", "GSM7916492", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "Lb 3", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916492", "GSM7916492: Lb 3; Danio rerio; ncRNA Seq", "GSM7916492 r1", "GSM7916492", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X17_160303_D00294_0224_AC95NJANXX_6.cutadapt.se.19_100.fastq.gz", "fastq", 900287704.0, 31947371.0, "GSM7916492 r1", "0:28.18", "A:224093089;C:188919051;G:262824615;T:224407166;N:43783", 28, null, null, null, 224093089, 188919051, 262824615, 224407166, 43783, "SRX22630093", "SRS19628575", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.67003, null, 0.17024, null, 0.87095, null, 0.6869, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29001, "SRR26936246", "SRX22630092", "SRS19628574", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 3", "GSM7916491", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Hb 3", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916491", "GSM7916491: Hb 3; Danio rerio; ncRNA Seq", "GSM7916491 r1", "GSM7916491", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X16_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 80986783.0, 3427704.0, "GSM7916491 r1", "0:23.63", "A:18164838;C:19014879;G:24153410;T:19641723;N:11933", 23, null, null, null, 18164838, 19014879, 24153410, 19641723, 11933, "SRX22630092", "SRS19628574", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.83312, null, 0.24402, null, 0.88749, null, 0.63345, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29002, "SRR26936247", "SRX22630091", "SRS19628573", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 3", "GSM7916490", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "La 3", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916490", "GSM7916490: La 3; Danio rerio; ncRNA Seq", "GSM7916490 r1", "GSM7916490", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X15_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 148933985.0, 6314805.0, "GSM7916490 r1", "0:23.58", "A:39058546;C:30363738;G:44242466;T:35240575;N:28660", 23, null, null, null, 39058546, 30363738, 44242466, 35240575, 28660, "SRX22630091", "SRS19628573", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.41302, null, 0.13369, null, 0.89802, null, 0.57553, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29003, "SRR26936248", "SRX22630090", "SRS19628572", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 2", "GSM7916489", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 2", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916489", "GSM7916489: La 2; Danio rerio; ncRNA Seq", "GSM7916489 r1", "GSM7916489", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X14_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 538382421.0, 23079847.0, "GSM7916489 r1", "0:23.33", "A:119659971;C:112896468;G:162693210;T:143063074;N:69698", 23, null, null, null, 119659971, 112896468, 162693210, 143063074, 69698, "SRX22630090", "SRS19628572", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.81532, null, 0.23945, null, 0.8758, null, 0.62425, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29004, "SRR26936249", "SRX22630089", "SRS19628571", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 1", "GSM7916488", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 1", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916488", "GSM7916488: Ha 1; Danio rerio; ncRNA Seq", "GSM7916488 r1", "GSM7916488", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X13_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 761541737.0, 32310434.0, "GSM7916488 r1", "0:23.57", "A:182485471;C:173949932;G:214306916;T:190683160;N:116258", 23, null, null, null, 182485471, 173949932, 214306916, 190683160, 116258, "SRX22630089", "SRS19628571", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.82936, null, 0.23022, null, 0.85098, null, 0.59571, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29005, "SRR26936250", "SRX22630088", "SRS19628570", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 2", "GSM7916487", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 2", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916487", "GSM7916487: Lb 2; Danio rerio; ncRNA Seq", "GSM7916487 r1", "GSM7916487", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X12_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 559417322.0, 23757934.0, "GSM7916487 r1", "0:23.55", "A:126286771;C:106333997;G:170445137;T:156287131;N:64286", 23, null, null, null, 126286771, 106333997, 170445137, 156287131, 64286, "SRX22630088", "SRS19628570", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85098, null, 0.26224, null, 0.8608, null, 0.59344, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29006, "SRR26936251", "SRX22630087", "SRS19628569", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 1", "GSM7916486", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Lb 1", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916486", "GSM7916486: Lb 1; Danio rerio; ncRNA Seq", "GSM7916486 r1", "GSM7916486", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X11_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 498695572.0, 21269833.0, "GSM7916486 r1", "0:23.45", "A:122716879;C:84997892;G:144626268;T:146292630;N:61903", 23, null, null, null, 122716879, 84997892, 144626268, 146292630, 61903, "SRX22630087", "SRS19628569", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84251, null, 0.1958, null, 0.8591, null, 0.61008, null, 24, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29007, "SRR26936252", "SRX22630086", "SRS19628568", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 10", "GSM7916485", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "Hb 10", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916485", "GSM7916485: Hb 10; Danio rerio; ncRNA Seq", "GSM7916485 r1", "GSM7916485", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X10_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 686865211.0, 29320389.0, "GSM7916485 r1", "0:23.43", "A:156131568;C:132162427;G:201526230;T:196961742;N:83244", 23, null, null, null, 156131568, 132162427, 201526230, 196961742, 83244, "SRX22630086", "SRS19628568", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85707, null, 0.27856, null, 0.85648, null, 0.59717, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29008, "SRR26936253", "SRX22630085", "SRS19628567", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 9", "GSM7916484", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "La 9", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916484", "GSM7916484: La 9; Danio rerio; ncRNA Seq", "GSM7916484 r1", "GSM7916484", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X9_160303_D00294_0224_AC95NJANXX_5.cutadapt.se.19_100.fastq.gz", "fastq", 561289514.0, 23860643.0, "GSM7916484 r1", "0:23.52", "A:140848879;C:98838555;G:161520871;T:160013845;N:67364", 23, null, null, null, 140848879, 98838555, 161520871, 160013845, 67364, "SRX22630085", "SRS19628567", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85507, null, 0.17768, null, 0.86969, null, 0.64792, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29009, "SRR26936254", "SRX22630084", "SRS19628566", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 8", "GSM7916483", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "La 8", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916483", "GSM7916483: La 8; Danio rerio; ncRNA Seq", "GSM7916483 r1", "GSM7916483", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X8_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 458491681.0, 16224249.0, "GSM7916483 r1", "0:28.26", "A:99631677;C:90884289;G:139467457;T:128470855;N:37403", 28, null, null, null, 99631677, 90884289, 139467457, 128470855, 37403, "SRX22630084", "SRS19628566", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.81704, null, 0.21909, null, 0.84762, null, 0.6293, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29010, "SRR26936255", "SRX22630083", "SRS19628565", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 9", "GSM7916482", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "Ha 9", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916482", "GSM7916482: Ha 9; Danio rerio; ncRNA Seq", "GSM7916482 r1", "GSM7916482", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X7_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 574511047.0, 20295283.0, "GSM7916482 r1", "0:28.31", "A:134481373;C:122719422;G:169313406;T:147944946;N:51900", 28, null, null, null, 134481373, 122719422, 169313406, 147944946, 51900, "SRX22630083", "SRS19628565", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.81932, null, 0.19984, null, 0.85987, null, 0.58268, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29011, "SRR26936256", "SRX22630082", "SRS19628564", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 8", "GSM7916481", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 8", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916481", "GSM7916481: Lb 8; Danio rerio; ncRNA Seq", "GSM7916481 r1", "GSM7916481", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X6_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 1086899780.0, 37486748.0, "GSM7916481 r1", "0:28.99", "A:219996636;C:232899819;G:335644980;T:298269921;N:88424", 28, null, null, null, 219996636, 232899819, 335644980, 298269921, 88424, "SRX22630082", "SRS19628564", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.86943, null, 0.2105, null, 0.84461, null, 0.67703, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29012, "SRR26936257", "SRX22630081", "SRS19628563", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 9", "GSM7916480", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 9", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916480", "GSM7916480: Hb 9; Danio rerio; ncRNA Seq", "GSM7916480 r1", "GSM7916480", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X5_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 1144093618.0, 39048750.0, "GSM7916480 r1", "0:29.30", "A:223769668;C:238953593;G:358148504;T:323130325;N:91528", 29, null, null, null, 223769668, 238953593, 358148504, 323130325, 91528, "SRX22630081", "SRS19628563", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.87445, null, 0.1906, null, 0.87237, null, 0.70919, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29013, "SRR26936258", "SRX22630080", "SRS19628562", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 7", "GSM7916515", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 7", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916515", "GSM7916515: Hb 7; Danio rerio; ncRNA Seq", "GSM7916515 r1", "GSM7916515", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X40_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 263782568.0, 9802454.0, "GSM7916515 r1", "0:26.91", "A:59378855;C:53589034;G:83219251;T:67574216;N:21212", 26, null, null, null, 59378855, 53589034, 83219251, 67574216, 21212, "SRX22630080", "SRS19628562", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.80146, null, 0.31524, null, 0.81008, null, 0.47305, null, 30, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29014, "SRR26936260", "SRX22630079", "SRS19628561", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 8", "GSM7916514", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 8", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916514", "GSM7916514: Ha 8; Danio rerio; ncRNA Seq", "GSM7916514 r1", "GSM7916514", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X39_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 252119227.0, 9309447.0, "GSM7916514 r1", "0:27.08", "A:53293803;C:51577689;G:79148986;T:68078043;N:20706", 27, null, null, null, 53293803, 51577689, 79148986, 68078043, 20706, "SRX22630079", "SRS19628561", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.75593, null, 0.29042, null, 0.83412, null, 0.59657, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29015, "SRR26936261", "SRX22630078", "SRS19628560", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 6", "GSM7916513", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 6", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916513", "GSM7916513: Hb 6; Danio rerio; ncRNA Seq", "GSM7916513 r1", "GSM7916513", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X38_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 516408240.0, 19719085.0, "GSM7916513 r1", "0:26.19", "A:112791146;C:102652986;G:160354602;T:140566375;N:43131", 26, null, null, null, 112791146, 102652986, 160354602, 140566375, 43131, "SRX22630078", "SRS19628560", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.80401, null, 0.31982, null, 0.83765, null, 0.57755, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29016, "SRR26936262", "SRX22630077", "SRS19628559", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 7", "GSM7916512", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 7", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916512", "GSM7916512: Ha 7; Danio rerio; ncRNA Seq", "GSM7916512 r1", "GSM7916512", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X37_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 554171558.0, 20779285.0, "GSM7916512 r1", "0:26.67", "A:125256371;C:111354628;G:172197000;T:145317427;N:46132", 26, null, null, null, 125256371, 111354628, 172197000, 145317427, 46132, "SRX22630077", "SRS19628559", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.81035, null, 0.28326, null, 0.82933, null, 0.62525, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29017, "SRR26936263", "SRX22630076", "SRS19628558", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 10", "GSM7916511", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 10", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916511", "GSM7916511: Lb 10; Danio rerio; ncRNA Seq", "GSM7916511 r1", "GSM7916511", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X36_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 983846643.0, 32513493.0, "GSM7916511 r1", "0:30.26", "A:181840038;C:211101778;G:320659770;T:270174775;N:70282", 30, null, null, null, 181840038, 211101778, 320659770, 270174775, 70282, "SRX22630076", "SRS19628558", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.88133, null, 0.15829, null, 0.86324, null, 0.67761, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29018, "SRR26936264", "SRX22630075", "SRS19628557", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 9", "GSM7916510", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low2|geo loc name:missing|collection date:missing", "Lb 9", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low2", "GSM7916510", "GSM7916510: Lb 9; Danio rerio; ncRNA Seq", "GSM7916510 r1", "GSM7916510", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X35_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 1077131964.0, 37869598.0, "GSM7916510 r1", "0:28.44", "A:210508796;C:220304812;G:327237157;T:319001223;N:79976", 28, null, null, null, 210508796, 220304812, 327237157, 319001223, 79976, "SRX22630075", "SRS19628557", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84871, null, 0.22867, null, 0.83968, null, 0.66027, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29019, "SRR26936265", "SRX22630074", "SRS19628556", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Lb 7", "GSM7916509", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "Lb 7", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916509", "GSM7916509: Lb 7; Danio rerio; ncRNA Seq", "GSM7916509 r1", "GSM7916509", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X34_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 1203153474.0, 42565421.0, "GSM7916509 r1", "0:28.27", "A:269760359;C:263088083;G:348288367;T:321910116;N:106549", 28, null, null, null, 269760359, 263088083, 348288367, 321910116, 106549, "SRX22630074", "SRS19628556", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.82319, null, 0.21661, null, 0.82432, null, 0.65954, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29020, "SRR26936266", "SRX22630073", "SRS19628555", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 7", "GSM7916508", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 7", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916508", "GSM7916508: La 7; Danio rerio; ncRNA Seq", "GSM7916508 r1", "GSM7916508", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X33_160303_D00294_0224_AC95NJANXX_8.cutadapt.se.19_100.fastq.gz", "fastq", 1137464666.0, 42434385.0, "GSM7916508 r1", "0:26.81", "A:240256314;C:218420241;G:336730784;T:341968066;N:89261", 26, null, null, null, 240256314, 218420241, 336730784, 341968066, 89261, "SRX22630073", "SRS19628555", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84647, null, 0.26357, null, 0.85313, null, 0.67665, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29021, "SRR26936259", "SRX22630072", "SRS19628554", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Hb 8", "GSM7916479", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High2|geo loc name:missing|collection date:missing", "Hb 8", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High2", "GSM7916479", "GSM7916479: Hb 8; Danio rerio; ncRNA Seq", "GSM7916479 r1", "GSM7916479", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X4_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 1014850001.0, 36540733.0, "GSM7916479 r1", "0:27.77", "A:205870762;C:199482442;G:294628769;T:314783528;N:84500", 27, null, null, null, 205870762, 199482442, 294628769, 314783528, 84500, "SRX22630072", "SRS19628554", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84303, null, 0.28884, null, 0.81692, null, 0.66059, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29022, "SRR26936268", "SRX22630071", "SRS19628553", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "La 10", "GSM7916478", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:Low1|geo loc name:missing|collection date:missing", "La 10", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:Low1", "GSM7916478", "GSM7916478: La 10; Danio rerio; ncRNA Seq", "GSM7916478 r1", "GSM7916478", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X3_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 916186556.0, 32659639.0, "GSM7916478 r1", "0:28.05", "A:216314501;C:191651870;G:267047552;T:241092719;N:79914", 28, null, null, null, 216314501, 191651870, 267047552, 241092719, 79914, "SRX22630071", "SRS19628553", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.84312, null, 0.23836, null, 0.83132, null, 0.57754, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29023, "SRR26936269", "SRX22630070", "SRS19628552", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 10", "GSM7916477", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 10", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916477", "GSM7916477: Ha 10; Danio rerio; ncRNA Seq", "GSM7916477 r1", "GSM7916477", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X2_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 858990742.0, 30463457.0, "GSM7916477 r1", "0:28.20", "A:182799146;C:179417249;G:265490509;T:231201694;N:82144", 28, null, null, null, 182799146, 179417249, 265490509, 231201694, 82144, "SRX22630070", "SRS19628552", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.67221, null, 0.19137, null, 0.87986, null, 0.67831, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "Cell Line", "Cell Line"], [29024, "SRR26936270", "SRX22630069", "SRS19628551", "SRP473892", "PRJNA1044439", "Social stress in fathers affects sperm small RNA and offspring transcriptome profiles", "GSE248535", "Transcriptome Analysis", "Environmental changes may affect paternal condition and following generations but the underlying mechanisms are poorly understood. Male male competition induces a physiological stress response and affects male hormone levels  ejaculate traits and development in their offspring. Here we investigated the role of sperm mediated small RNAs in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes and transposable elements TEs at this key developmental stage. We sequenced micro  mi and Piwi interacting piRNAs in sperm and the full transcriptome in the embryos and ran differential expression analyses. We identified differentially expressed sperm mi  and piRNAs  with the strongest effects observed in sperm of males switching from high to low competition environments. We identified 612 differentially expressed genes in the embryos. These results confirm that the social environment does not only affect males but also the molecular ecology of their sperm and the gene expression in their offspring suggesting a putative role of sRNAs. Overall design: This data deposit includes the small RNA seq data for this research. Male zebrafish were subject to high and low social stress environments  with sperm samples collected  RNA extracted and sent for small RNA sequencing.", null, "pubmed:40121340", null, "Ha 2", "GSM7916476", null, "tissue:sperm|cell line:sperm|genotype:WT|treatment:High1|geo loc name:missing|collection date:missing", "Ha 2", "Reads were trimmed  aligned with PatMan and then count matrices assembled before DESeq2 analyses Assembly: GRCz10 Supplementary files format and content: piRNA raw counts.csv  raw counts of a subset of 24 out of the 40 samples that were analysed. These 24 were chosen due to noise observed in PCA clustering. Supplementary files format and content: mirna raw counts.csv  raw counts for 39/40 samples as one sample failed to progress through our pipeline to the same high quality as the other 39  so this sample was omitted from analyses.", "sperm", null, "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "cell line:sperm|genotype:WT|treatment:High1", "GSM7916476", "GSM7916476: Ha 2; Danio rerio; ncRNA Seq", "GSM7916476 r1", "GSM7916476", "1", "Total RNA extraction New England BioLabs kit NEBNext\u00aeMultiplex Small RNA Library Prep Set for Illumina\u00ae Set 1 and 2 NEB #E7300 and NEB #E7580 small RNA library prep for Illumina", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP473892", null, null, "12235X1_160303_D00294_0224_AC95NJANXX_4.cutadapt.se.19_100.fastq.gz", "fastq", 262855265.0, 9317037.0, "GSM7916476 r1", "0:28.21", "A:59555006;C:56655912;G:79385169;T:67236972;N:22206", 28, null, null, null, 59555006, 56655912, 79385169, 67236972, 22206, "SRX22630069", "SRS19628551", "SRA1756943", "University of East Anglia", "University of East Anglia", 1, 0.85088, null, 0.21543, null, 0.84102, null, 0.63415, null, 28, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-11-23", "Undetermined", "Embryo", "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. 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The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. 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Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "1h1_clean_R1.fq.gz 1h1_clean_R2.fq.gz", "fastq fastq", 6177620796.0, 20455698.0, "1h1 clean R1.fq.gz", "0:151 1:151", "A:1646973061;C:1422549043;G:1441385824;T:1663912518;N:2800350", 151, 151, null, null, 1646973061, 1422549043, 1441385824, 1663912518, 2800350, "SRX5740639", "SRS4676160", "SRA879791", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93085, 0.92866, 0.12633, 0.12579, 0.75812, 0.76136, 0.48992, 0.50959, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49829, "SRR8961088", "SRX5740638", "SRS4676159", "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, "1h 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", "1h 5", "1h 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, "1h2_clean_R2.fq.gz 1h2_clean_R1.fq.gz", "fastq fastq", 5616651266.0, 18598183.0, "1h2 clean R1.fq.gz", "0:151 1:151", "A:1492544948;C:1296049637;G:1317613246;T:1507292547;N:3150888", 151, 151, null, null, 1492544948, 1296049637, 1317613246, 1507292547, 3150888, "SRX5740638", "SRS4676159", "SRA879791", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93168, 0.93082, 0.12771, 0.12751, 0.75653, 0.75964, 0.508, 0.51051, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49830, "SRR8959882", "SRX5739436", "SRS4675912", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #6", "ck 6", null, "replicate:replicate=#6|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 6", "ck 6", "ck 6", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. 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, "CK3_clean_R1.fq.gz CK3_clean_R2.fq.gz", "fastq fastq", 6417346282.0, 21249491.0, "CK3 clean R1.fq.gz", "0:151 1:151", "A:1753073270;C:1445910840;G:1452693305;T:1762084157;N:3584710", 151, 151, null, null, 1753073270, 1445910840, 1452693305, 1762084157, 3584710, "SRX5739436", "SRS4675912", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92653, 0.92662, 0.11696, 0.11682, 0.75166, 0.75379, 0.50678, 0.50594, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49831, "SRR8959883", "SRX5739435", "SRS4675911", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #4", "ck 4", null, "replicate:replicate=#4|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 4", "ck 4", "ck 4", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK1_clean_R1.fq.gz CK1_clean_R2.fq.gz", "fastq fastq", 5659831830.0, 18741165.0, "CK1 clean R1.fq.gz", "0:151 1:151", "A:1532952307;C:1289729700;G:1295220307;T:1538761250;N:3168266", 151, 151, null, null, 1532952307, 1289729700, 1295220307, 1538761250, 3168266, "SRX5739435", "SRS4675911", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92518, 0.92535, 0.11332, 0.11378, 0.74919, 0.75235, 0.50223, 0.49803, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49832, "SRR8959884", "SRX5739434", "SRS4675910", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "control  replicate #5", "ck 5", null, "replicate:replicate=#5|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "replicate 5", "ck 5", "ck 5", "Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "CK2_clean_R1.fq.gz CK2_clean_R2.fq.gz", "fastq fastq", 5880727616.0, 19472608.0, "CK2 clean R1.fq.gz", "0:151 1:151", "A:1575999691;C:1352057289;G:1366253556;T:1583120335;N:3296745", 151, 151, null, null, 1575999691, 1352057289, 1366253556, 1583120335, 3296745, "SRX5739434", "SRS4675910", "SRA879767", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.93653, 0.9349, 0.09037, 0.09026, 0.76262, 0.76572, 0.51143, 0.50376, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-04-26", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49833, "SRR8133154", "SRX4954244", "SRS3995636", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #1", "24h 1", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour   replicate #1", "24h 1", "24h 1", "Sequencing libraries were generated using the  TruSeq RNA Sample Preparation Kit Illumina according to manufacturers  instructions. Three micrograms of total RNA were used as initial material for  library preparation. Briefly  mRNA was purified using poly T oligo attached  magnetic beads. Fragmentation of mRNA was conducted using divalent cations  under elevated temperature in the Illumina proprietary fragmentation buffer.  First strand cDNA was synthesized using random oligonucleotides and  SuperScript II. Second strand cDNA was subsequently synthesized using DNA  Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments   Illumina PE adapter oligonucleotides were ligated and the library fragments  were purified using the AMPure XP system Beckman Coulter. DNA fragments  with ligated adaptors on both ends were selectively enriched using Illumina  PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified  AMPure XP system and quantified using the Agilent high sensitivity DNA  assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were  then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina  by Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-1_R1.fastq.gz 24h-1_R2.fastq.gz", "fastq fastq", 6408674352.0, 21220776.0, "24h 1 R1.fastq.gz", "0:151 1:151", "A:1752104547;C:1447174976;G:1451968217;T:1757298923;N:127689", 151, 151, null, null, 1752104547, 1447174976, 1451968217, 1757298923, 127689, "SRX4954244", "SRS3995636", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.9212, 0.91969, 0.14419, 0.14446, 0.73677, 0.74363, 0.49228, 0.49725, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-10-30", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49834, "SRR8133155", "SRX4954243", "SRS3995635", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "24h 2", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #2", "24h 2", "24h 2", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-2_R1.fastq.gz 24h-2_R2.fastq.gz", "fastq fastq", 6331528754.0, 20965327.0, "24h 2 R1.fastq.gz", "0:151 1:151", "A:1725083256;C:1436372645;G:1442486884;T:1727457912;N:128057", 151, 151, null, null, 1725083256, 1436372645, 1442486884, 1727457912, 128057, "SRX4954243", "SRS3995635", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.92281, 0.92303, 0.13905, 0.14045, 0.73708, 0.74401, 0.50843, 0.50295, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49835, "SRR8133156", "SRX4954242", "SRS3995634", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "24h 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "24h 3", "24h 3", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. Ltd.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP166817", null, null, "24h-3_R1.fastq.gz 24h-3_R2.fastq.gz", "fastq fastq", 6723114940.0, 22261970.0, "24h 3 R1.fastq.gz", "0:151 1:151", "A:1833689339;C:1522824611;G:1529534136;T:1836931192;N:135662", 151, 151, null, null, 1833689339, 1522824611, 1529534136, 1836931192, 135662, "SRX4954242", "SRS3995634", "SRA800477", "Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute", "Chinese Academy of Fishery Sciences", 2, 0.91356, 0.91347, 0.13955, 0.14059, 0.73898, 0.74399, 0.49776, 0.50087, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-01-01", "Undetermined", "Undetermined", "Cell Line", "Cell Line"], [49836, "SRR8133151", "SRX4954241", "SRS3995633", "SRP166817", "PRJNA498018", "Danio rerio strain:ZFL cell line Genome sequencing", "PRJNA498018", "Whole Genome Sequencing", "Transcriptional responses of ZFL exposed to microcystin LR", null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "12h 3", null, "isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour  replicate #3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sample exposed to microcystin for xxx hour  replicate #3", "12h 3", "12h 3", "Sequencing libraries were generated using the TruSeq RNA Sample  Preparation Kit Illumina according to manufacturers instructions. Three  micrograms of total RNA were used as initial material for library  preparation. Briefly  mRNA was purified using poly T oligo attached magnetic  beads. Fragmentation of mRNA was conducted using divalent cations under  elevated temperature in the Illumina proprietary fragmentation buffer. First  strand cDNA was synthesized using random oligonucleotides and SuperScript II.  Second strand cDNA was subsequently synthesized using DNA Polymerase I and  RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE  adapter oligonucleotides were ligated and the library fragments were purified  using the AMPure XP system Beckman Coulter. DNA fragments with ligated  adaptors on both ends were selectively enriched using Illumina PCR Primer  Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP  system and quantified using the Agilent high sensitivity DNA assay on a  Bioanalyzer 2100 system Agilent. The sequencing libraries were then  sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by  Shanghai Personal Biotechnology Cp. 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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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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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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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"experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "Cell Line"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 63, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_strategy=ncRNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "PCR", "label": "PCR", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_selection=PCR", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_selection=size+fractionation", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 16, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_selection=cDNA", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_selection=Oligo-dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 63, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 52, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 46, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Cell+Line", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "Cell Line", "label": "Cell Line", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&tissue_curation_coarse=Cell+Line", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "Cell Line", "label": "Cell Line", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line", "results": [{"value": "unknown", "label": "unknown", "count": 109, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&technology=bulk", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "49844", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Cell+Line&_next=49844", "private": false, "allow_execute_sql": true, "query_ms": 108.13477700139629}