{"database": "metadata", "table": "run_metadata", "rows": [[59354, "SRR11862877", "SRX8413247", "SRS6725557", "SRP265077", "PRJNA635603", "Paternal effects in a wild type zebrafish implicate a role of sperm derived small RNAs", "PRJNA635603", "Other", "A growing body of evidence points to the paternal environment pre fertilisation having an important influence on offspring phenotype  mediated via noncoding RNA e.g. microRNA transmitted in spermatozoa. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors before mating and assessing the behavioural and endocrine responses of their offspring. We found that post males are exposed to stress  their larval offspring show weakened responses to stressors. We subsequently applied small RNA sequencing to ascertain whether stress affected patterns of small RNA abundance in paternal sperm  which may in turn have influenced offspring development.", null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchD", "library 7 batchD control", null, "strain:London Wildtype|dev stage:Adult|sex:male|tissue:not applicable|cell type:Spermatozoa|geo loc name:United Kingdom: Sheffield|treatment:Control|filename:7SMALL GTCCGC L002 R1 001.fastq.gz|batch:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA seq of zebrafish spermatozoa  from control adult male batchD", "7SMALL GTCCGC L002 R1 001.fastq.gz", "7SMALL GTCCGC L002 R1 001.fastq.gz", "Adult male London Wildtype LWT zebrafish aged 6 month 10 month were housed individually in tanks on a recirculatory system with water heated to 26C and kept on a 12:12h light / dark cycle. Animals were fed brine shrimp or flake food twice daily. Adult males were subjected to a chronic stress constituting 20 minutes of alarm substance exposure  periodic net chasing  or bright light exposure for 12 14 days. Control males were handled in an identical fashion but not subjected to the stressors. Four to five individuals in both control and stress groups comprised one experimental batch. A total of six experimental batches were carried out.Spermatozoa were collected from euthanized adult males by disruption of dissected testes in ice cold Hanks balanced salt solution HBSS to derive a testicular cell suspension  which was then centrifuged 800 xg for 40 min on top of a 40/80 Percoll gradient to separate spermatozoa from larger cells. The sperm precipitate washed in ice cold HBSS  pelleted 1000 xg for 10 mins  re suspended in Tri reagent and stored at  80C until RNA extraction. Total RNA was extracted following the Tri reagent protocol with the addition of an overnight precipitation step with glycogen in 2 propanol at  20C. Each sperm RNA sample comprised a pool of multiple individuals within the experimental batches such that each of six batches contributed one replicate pair control and stress  for a total of 12 biological samples.Small RNA sequencing libraries were prepared using the SomaGenics Santa Cruz Real Seq Biofluids kit following the manufacturers instructions  using a minimum of 2.5 ng of input total RNA. Twenty PCR cycles were performed to amplify the reverse transcription product. The quality of the prepared libraries was examined using the Agilent Hi sensitivity DNA chip prior to the individual libraries being pooled to a concentration of 4nM for Illumina sequencing. Sequencing was carried out on an Illumina HiSeq 2500 using SBS v3 chemistry and single end 65 base reads.### PLEASE NOTE ###The supplied FASTQ files are raw data which still contain the adaptor sequence TGGAATTCTCGGGTGCCAAGG.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP265077", null, null, "7SMALL_GTCCGC_L002_R1_001.fastq.gz", "fastq", 871937682.0, 13211177.0, "7SMALL GTCCGC L002 R1 001.fastq.gz", "0:66", "A:187309754;C:240910478;G:236157154;T:207547961;N:12335", 66, null, null, null, 187309754, 240910478, 236157154, 207547961, 12335, "SRX8413247", "SRS6725557", "SRA1080712", "University of Tartu|Department of Pathophysiology", "University of Tartu", 1, 0.00388, null, 0.00062, null, 0.99622, null, 0.86525, null, 66, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Estonia", "2020-05-28", "Adult", "Adult", "Multi-tissue", "Multi-system"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["59354"], "units": {}, "query_ms": 9.856379998382181}