{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and experiment.library_strategy = \"ncRNA-Seq\"", "rows": [[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. 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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. 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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. 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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. 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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. 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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. 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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. 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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"], [44967, "SRR6345660", "SRX3442976", "SRS2733636", "SRP126106", "PRJNA421016", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [small RNA]", "GSE107682", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Zebrafish were grown under standard conditions. Total ovary or size selected Oocytes were used to extact RNA from het of tdrd6a mutant fish.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "smRNA seq library of ovary from tdrd6a mut fish", "GSM2875719", null, "source name:Ovary from tdrd6a mut fish|tissue:whole ovary|genotype:tdrd6a mutant", "smRNA seq library of ovary from tdrd6a mut fish", "1. Adapter trimming with cutadapt  O 8  m 26  M 38  a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 2. Low quality read filtering with fastq quality filter   q 20  p 100  Q 33. 3. Duplicate reads were collapsed using the unique molecule identifiers UMIs added during library preparation 4 random bases at both the five prime and three prime end  using a custom bash script. 4. UMIs were trimmed with seqtk trimfq  b 4  a 4 5. Reads with less than 15 nt in length were filtered out with seqtk seq  L 15\u00a0 6. Mapping was done to Zebrafish  Danio rerio  genome assembly Zv9 with bowtie v0.12.8   tryhard   best   strata   chunkmbs 256  v 1  M 5. 7. Bigwig tracks normalized to the number of mapped reads were created using genomeCoverageBed  bg  split  scale bedtools 2.25.0 followed by bedGraphToBigWig Kent utilities.\u00a0 \u00a0 8. Mapped reads converted to bed with bamToBed where intersected with the locations of transposable elements LINE  SINE  LTR and DNA downloaded from the UCSC genome browser repeat masker track  Zv9 using bedtools intersect  a reads  b transposons  wa  wb  bed  f 1.0  nonamecheck to keep both the read and the transposon information. The arguments  s/ S were also set to find reads mapping sense or antisense to the transposons. Results are in data file transposons counts.txt.gz Genome build: Zv9 Supplementary files format and content: transposons counts.txt.gz is a compressed tab delimited file. Each line corresponds a read that overlaps and annotated transposon. The fields chr re  start re  end re  repFamily  repName strand re  and repClass represent the location and classification of the repeat elements as described in the RepeatMasker track of UCSC. Feature is whether they are DNA or RNA transposons  and readlength the length of the read that. Sample is the sample name  and Mapping whether teh reads mapped sense or antisense in relation to the transposon it maps to.\u00a0 Supplementary files format and content: Files ending in .bw are bigwig tracks.", "Ovary from tdrd6a mut fish", null, "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", null, "tissue:whole ovary|genotype:tdrd6a mutant", "GSM2875719", "GSM2875719: smRNA seq library of ovary from tdrd6a mut fish; Danio rerio; ncRNA Seq", "GSM2875719", null, "1", "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", "GEO Accession:GSM2875719", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP126106", null, null, "Tdrd6a-mut-ovary-input-Adult.fastq.gz", "fastq", 817885062.0, 16036962.0, "GSM2875719 r1", "0:51", "A:212456064;C:163491733;G:233627239;T:208262707;N:47319", 51, null, null, null, 212456064, 163491733, 233627239, 208262707, 47319, "SRX3442976", "SRS2733636", "SRA636010", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.46308, null, 0.13668, null, 0.83587, null, 0.79104, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2017-12-04", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [44968, "SRR6345659", "SRX3442975", "SRS2733637", "SRP126106", "PRJNA421016", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [small RNA]", "GSE107682", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Zebrafish were grown under standard conditions. Total ovary or size selected Oocytes were used to extact RNA from het of tdrd6a mutant fish.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "smRNA seq library of ovary from tdrd6a het fish", "GSM2875718", null, "source name:Ovary from tdrd6a het fish|tissue:whole ovary|genotype:tdrd6a heterozygous", "smRNA seq library of ovary from tdrd6a het fish", "1. Adapter trimming with cutadapt  O 8  m 26  M 38  a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 2. Low quality read filtering with fastq quality filter   q 20  p 100  Q 33. 3. Duplicate reads were collapsed using the unique molecule identifiers UMIs added during library preparation 4 random bases at both the five prime and three prime end  using a custom bash script. 4. UMIs were trimmed with seqtk trimfq  b 4  a 4 5. Reads with less than 15 nt in length were filtered out with seqtk seq  L 15\u00a0 6. Mapping was done to Zebrafish  Danio rerio  genome assembly Zv9 with bowtie v0.12.8   tryhard   best   strata   chunkmbs 256  v 1  M 5. 7. Bigwig tracks normalized to the number of mapped reads were created using genomeCoverageBed  bg  split  scale bedtools 2.25.0 followed by bedGraphToBigWig Kent utilities.\u00a0 \u00a0 8. Mapped reads converted to bed with bamToBed where intersected with the locations of transposable elements LINE  SINE  LTR and DNA downloaded from the UCSC genome browser repeat masker track  Zv9 using bedtools intersect  a reads  b transposons  wa  wb  bed  f 1.0  nonamecheck to keep both the read and the transposon information. The arguments  s/ S were also set to find reads mapping sense or antisense to the transposons. Results are in data file transposons counts.txt.gz Genome build: Zv9 Supplementary files format and content: transposons counts.txt.gz is a compressed tab delimited file. Each line corresponds a read that overlaps and annotated transposon. The fields chr re  start re  end re  repFamily  repName strand re  and repClass represent the location and classification of the repeat elements as described in the RepeatMasker track of UCSC. Feature is whether they are DNA or RNA transposons  and readlength the length of the read that. Sample is the sample name  and Mapping whether teh reads mapped sense or antisense in relation to the transposon it maps to.\u00a0 Supplementary files format and content: Files ending in .bw are bigwig tracks.", "Ovary from tdrd6a het fish", null, "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", null, "tissue:whole ovary|genotype:tdrd6a heterozygous", "GSM2875718", "GSM2875718: smRNA seq library of ovary from tdrd6a het fish; Danio rerio; ncRNA Seq", "GSM2875718", null, "1", "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", "GEO Accession:GSM2875718", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP126106", null, null, "Tdrd6a-het-ovary-input-Adult.fastq.gz", "fastq", 1452353571.0, 28477521.0, "GSM2875718 r1", "0:51", "A:397993735;C:284194126;G:396142390;T:373939235;N:84085", 51, null, null, null, 397993735, 284194126, 396142390, 373939235, 84085, "SRX3442975", "SRS2733637", "SRA636010", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.3869, null, 0.1369, null, 0.86397, null, 0.77165, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2017-12-04", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [58545, "SRR13652352", "SRX10049115", "SRS8212343", "SRP253438", "PRJNA613601", "five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq  ssDRIP seq]", "GSE147253", "Other", "five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However  it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis  dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively  and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos  tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically  unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing   total RNA were extracted respectively from wildtype zebrafish embryos T\u00fcbingen Strain of 6 chosen stages  and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome  we performed ssDRIP seq with S9.6 antibody  which specifically recognize RNA:DNA hybrid.  Two replicates from wildtype embryos of 256c  sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control  which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes  and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation.", "parent bioproject:PRJNA753013", "pubmed:34797706", null, "256c ncRNA seq", "GSM5069282", null, "tissue:embryo|strain:Tubingen|developmental stage:256c stage|treatement:no", "256c ncRNA seq", "For data processing  reads were quality checked by FastQCVersion 0.11.8  and adaptors were cut off by Cutadapt Version 1.16  and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2  Version 2.3.4.1  count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA   tRNA database GtRNAdb  GRCz11", "embryo", null, "For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube  and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific  15596018. The lysate was centrifuged at 12 000 rpm for 10 min  and the supernatant was collected and mixed with 200 \u03bcl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4\u2103  the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min  followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at  80\u2103 until all samples were collected. Two pretreatment steps were included: First  purified total RNAs were treated with T4 Polynucleotide Kinase NEB  M0201S with ATP for 30 min at 37\u2103  then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3\u2019 cyclic phosphate group from the 3\u2019end of 5\u2019tRFls  and add phosphate group to the 5\u2019end of 3\u2019tRFs. In the second step  total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing:  Small RNA libraries  using 1 \u03bcg RNA each  were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research  then bands of 135 160 bp  about the length of 15 40 nt RNA ligated with both adaptors  were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc  pH 4.5  followed by precipitation by adding 2.5 volumes of ethanol.", null, "strain:Tubingen|developmental stage:256c stage|treatement:no", "GSM5069282", "GSM5069282: 256c ncRNA seq; Danio rerio; ncRNA Seq", "GSM5069282", null, "1", "For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube  and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific  15596018. The lysate was centrifuged at 12 000 rpm for 10 min  and the supernatant was collected and mixed with 200 \u03bcl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4\u2103  the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min  followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at  80\u2103 until all samples were collected. Two pretreatment steps were included: First  purified total RNAs were treated with T4 Polynucleotide Kinase NEB  M0201S with ATP for 30 min at 37\u2103  then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls  and add phosphate group to the five primeend of three primetRFs. In the second step  total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing:  Small RNA libraries  using 1 \u03bcg RNA each  were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research  then bands of 135 160 bp  about the length of 15 40 nt RNA ligated with both adaptors  were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc  pH 4.5  followed by precipitation by adding 2.5 volumes of ethanol.", "GEO Accession:GSM5069282", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP253438", null, null, "256c-RNA_seq.fq.gz", "fastq", 4634985600.0, 30899904.0, "GSM5069282 r1", "0:150 1:0", "A:815670917;C:820280105;G:2237895473;T:760861465;N:277640", 150, 0, null, null, 815670917, 820280105, 2237895473, 760861465, 277640, "SRX10049115", "SRS8212343", "SRA1056877", "GEO", "Anming Meng Lab, School of Life Science, Tsinghua University", 1, 0.67611, null, 0.16429, null, 0.8076, null, 0.58827, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2021-02-08", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [61688, "SRR13302966", "SRX9731824", "SRS7924603", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV\u25b3B2: Ago2 IP 3 dpi", "GSM4988099", null, "source name:zebrafish whole body|zebrafish background:AB|infection:NoV\u25b3B2|injection way:microinjection|tissue:zebrafish whole body", "NoV\u25b3B2: Ago2 IP 3 dpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "zebrafish background:AB|infection:NoV\u25b3B2|injection way:microinjection|tissue:zebrafish whole body", "GSM4988099", "GSM4988099: NoV\u25b3B2: Ago2 IP 3 dpi; Danio rerio; ncRNA Seq", "GSM4988099", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4988099", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "LY272.fq.gz", "fastq", 2608504950.0, 17390033.0, "GSM4988099 r1", "0:150 1:0", "A:741941121;C:669191911;G:747181676;T:450096994;N:93248", 150, 0, null, null, 741941121, 669191911, 747181676, 450096994, 93248, "SRX9731824", "SRS7924603", "SRA1151114", "GEO", "Fudan University", 1, 0.13133, null, 0.03425, null, 0.96802, null, 0.60095, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-12-24", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61689, "SRR12951276", "SRX9404383", "SRS7622158", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "SINV: zebrafish 3 dpi", "GSM4873784", null, "source name:zebrafish whole body|tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB", "SINV: zebrafish 3 dpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB", "GSM4873784", "GSM4873784: SINV: zebrafish 3 dpi; Danio rerio; ncRNA Seq", "GSM4873784", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873784", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP290217", null, null, "4_LY215.fq.gz", "fastq", 1328044600.0, 26560892.0, "GSM4873784 r1", "0:50 1:0", "A:383401484;C:303337306;G:339848340;T:301397824;N:59646", 50, 0, null, null, 383401484, 303337306, 339848340, 301397824, 59646, "SRX9404383", "SRS7622158", "SRA1151114", "GEO", "Fudan University", 1, 0.83242, null, 0.11559, null, 0.93634, null, 0.53516, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61690, "SRR12951275", "SRX9404382", "SRS7622159", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "VSV: zebrafish 24 hpi", "GSM4873783", null, "source name:zebrafish whole body|tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB", "VSV: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB", "GSM4873783", "GSM4873783: VSV: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873783", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873783", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "3_LY157.fq.gz", "fastq", 706147852.0, 29418915.0, "GSM4873783 r1", "0:24.00 1:0", "A:151681768;C:131117267;G:189016204;T:234316361;N:16252", 24, 0, null, null, 151681768, 131117267, 189016204, 234316361, 16252, "SRX9404382", "SRS7622159", "SRA1151114", "GEO", "Fudan University", 1, 0.92973, null, 0.12628, null, 0.90664, null, 0.45104, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61691, "SRR12951274", "SRX9404381", "SRS7622157", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV\u25b3B2: zebrafish 24 hpi", "GSM4873782", null, "source name:zebrafish whole body|tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB", "NoV\u25b3B2: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB", "GSM4873782", "GSM4873782: NoV\u25b3B2: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873782", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873782", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "2_LY156.fq.gz", "fastq", 748544818.0, 30779865.0, "GSM4873782 r1", "0:24.32 1:0", "A:166631198;C:138321792;G:208615021;T:234953337;N:23470", 24, 0, null, null, 166631198, 138321792, 208615021, 234953337, 23470, "SRX9404381", "SRS7622157", "SRA1151114", "GEO", "Fudan University", 1, 0.94115, null, 0.12368, null, 0.91076, null, 0.48684, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61692, "SRR12951273", "SRX9404380", "SRS7622156", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV: zebrafish 24 hpi", "GSM4873781", null, "source name:zebrafish whole body|tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB", "NoV: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB", "GSM4873781", "GSM4873781: NoV: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873781", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873781", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "1_LY155.fq.gz", "fastq", 594676353.0, 25019145.0, "GSM4873781 r1", "0:23.77 1:0", "A:129139705;C:108465388;G:162500636;T:194556532;N:14092", 23, 0, null, null, 129139705, 108465388, 162500636, 194556532, 14092, "SRX9404380", "SRS7622156", "SRA1151114", "GEO", "Fudan University", 1, 0.93471, null, 0.10892, null, 0.90814, null, 0.48797, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [67823, "SRR17335719", "SRX13511115", "SRS11405356", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF3", "GSM5754470", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754470", "GSM5754470: CPF3; Danio rerio; ncRNA Seq", "GSM5754470 r1", "GSM5754470", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF3_1.fq.gz CPF3_2.fq.gz", "fastq fastq", 12726241500.0, 42420805.0, "GSM5754470 r1", "0:150 1:150", "A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948", 150, 150, null, null, 3447613023, 2896153797, 2922038320, 3459698412, 737948, "SRX13511115", "SRS11405356", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89399, 0.89612, 0.38172, 0.37657, 0.66628, 0.66799, 0.53056, 0.53213, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67824, "SRR17335720", "SRX13511114", "SRS11405355", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF2", "GSM5754469", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754469", "GSM5754469: CPF2; Danio rerio; ncRNA Seq", "GSM5754469 r1", "GSM5754469", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF2_1.fq.gz CPF2_2.fq.gz", "fastq fastq", 14881715100.0, 49605717.0, "GSM5754469 r1", "0:150 1:150", "A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303", 150, 150, null, null, 4214905088, 3201163283, 3225795074, 4239665352, 186303, "SRX13511114", "SRS11405355", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87491, 0.87638, 0.40844, 0.40479, 0.67123, 0.67018, 0.49174, 0.48952, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67825, "SRR17335721", "SRX13511113", "SRS11405354", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF1", "GSM5754468", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754468", "GSM5754468: CPF1; Danio rerio; ncRNA Seq", "GSM5754468 r1", "GSM5754468", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF1_1.fq.gz CPF1_2.fq.gz", "fastq fastq", 16447798800.0, 54825996.0, "GSM5754468 r1", "0:150 1:150", "A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056", 150, 150, null, null, 4454573413, 3748270411, 3776995203, 4467442717, 517056, "SRX13511113", "SRS11405354", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89313, 0.8947, 0.35381, 0.35194, 0.64954, 0.64831, 0.51962, 0.52475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67826, "SRR17335722", "SRX13511112", "SRS11405353", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP3", "GSM5754467", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754467", "GSM5754467: CYP3; Danio rerio; ncRNA Seq", "GSM5754467 r1", "GSM5754467", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP3_1.fq.gz CYP3_2.fq.gz", "fastq fastq", 13417868100.0, 44726227.0, "GSM5754467 r1", "0:150 1:150", "A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295", 150, 150, null, null, 3645134270, 3041754103, 3084809543, 3645750889, 419295, "SRX13511112", "SRS11405353", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86122, 0.8638, 0.4112, 0.40785, 0.68738, 0.68519, 0.54768, 0.44856, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67827, "SRR17335723", "SRX13511111", "SRS11405352", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP2", "GSM5754466", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754466", "GSM5754466: CYP2; Danio rerio; ncRNA Seq", "GSM5754466 r1", "GSM5754466", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP2_1.fq.gz CYP2_2.fq.gz", "fastq fastq", 13096007700.0, 43653359.0, "GSM5754466 r1", "0:150 1:150", "A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913", 150, 150, null, null, 3638241155, 2892284693, 2925857490, 3639296449, 327913, "SRX13511111", "SRS11405352", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85953, 0.86247, 0.41975, 0.41734, 0.68174, 0.67862, 0.52504, 0.5324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67828, "SRR17335724", "SRX13511110", "SRS11405351", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP1", "GSM5754465", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754465", "GSM5754465: CYP1; Danio rerio; ncRNA Seq", "GSM5754465 r1", "GSM5754465", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP1_1.fq.gz CYP1_2.fq.gz", "fastq fastq", 16372872000.0, 54576240.0, "GSM5754465 r1", "0:150 1:150", "A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697", 150, 150, null, null, 4747286217, 3417115980, 3453793026, 4754530080, 146697, "SRX13511110", "SRS11405351", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85322, 0.85414, 0.46298, 0.45901, 0.68016, 0.67866, 0.47694, 0.47897, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67829, "SRR17335725", "SRX13511109", "SRS11405350", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont3", "GSM5754464", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754464", "GSM5754464: Cont3; Danio rerio; ncRNA Seq", "GSM5754464 r1", "GSM5754464", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont3_1.fq.gz Cont3_2.fq.gz", "fastq fastq", 15202443900.0, 50674813.0, "GSM5754464 r1", "0:150 1:150", "A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476", 150, 150, null, null, 4400470018, 3173803928, 3218623722, 4409335756, 210476, "SRX13511109", "SRS11405350", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86129, 0.84677, 0.45657, 0.44799, 0.67884, 0.68083, 0.48291, 0.4763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67830, "SRR17335726", "SRX13511108", "SRS11405349", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont2", "GSM5754463", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754463", "GSM5754463: Cont2; Danio rerio; ncRNA Seq", "GSM5754463 r1", "GSM5754463", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont2_1.fq.gz Cont2_2.fq.gz", "fastq fastq", 12927267600.0, 43090892.0, "GSM5754463 r1", "0:150 1:150", "A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179", 150, 150, null, null, 3474574877, 2959326086, 3006553706, 3486600752, 212179, "SRX13511108", "SRS11405349", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87695, 0.87907, 0.41673, 0.41416, 0.69266, 0.69266, 0.53339, 0.58145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67831, "SRR17335727", "SRX13511107", "SRS11405348", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont1", "GSM5754462", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754462", "GSM5754462: Cont1; Danio rerio; ncRNA Seq", "GSM5754462 r1", "GSM5754462", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont1_1.fq.gz Cont1_2.fq.gz", "fastq fastq", 18395362500.0, 61317875.0, "GSM5754462 r1", "0:150 1:150", "A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955", 150, 150, null, null, 5379624768, 3792463355, 3842313235, 5380702187, 258955, "SRX13511107", "SRS11405348", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.83439, 0.83446, 0.45703, 0.44894, 0.68828, 0.68578, 0.4957, 0.49639, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 57, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", 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