run_metadata: 14900
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 14900 | ERR12071830 | ERX11454455 | ERS16387697 | ERP151293 | PRJEB66218 | Social stress in Zebrafish sperm | b81525de-0f4f-4e41-8e34-f411e5590e7b | Other | Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm 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 at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm. | ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 | High stress | E113 13 | SAMEA114399005 | University of East Anglia | INSDC center name:University of East Anglia|Submitter Id:113 13|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:113 13|scientific name:Danio rerio | Illumina HiSeq X paired end sequencing | ena EXPERIMENT TAB 21 09 2023 13:32:15:293 66703 | 125bp | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq X | ERP151293 | Illumina HiSeq X paired end sequencing | ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21 | 113-13_S71_L007_R1_001.fastq.gz 113-13_S71_L007_R2_001.fastq.gz | fastq fastq | 18125498160.0 | 71926580.0 | ena RUN TAB 21 09 2023 13:32:15:293 66704 | 0:126 1:126 | A:3681246224;C:5316613237;G:5486708206;T:3609735923;N:31194570 | 126 | 126 | 3681246224 | 5316613237 | 5486708206 | 3609735923 | 31194570 | ERX11454455 | ERS16387697 | ERA27252154 | university of east anglia|European Nucleotide Archive | university of east anglia | 2 | 0.93952 | 0.93814 | 0.1717 | 0.17395 | 0.76627 | 0.76976 | 0.76533 | 0.72702 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | bulk | unknown | unknown | United Kingdom | 2023-09-21 | Undetermined | Embryo | Undetermined | Embryo Imprecise |