{"database": "metadata", "table": "run_metadata", "rows": [[60334, "SRR12194904", "SRX8707732", "SRS6984319", "SRP271280", "PRJNA645421", "Epigenomic RRBS analyses in brains of exposed F0 zebrafish and their unexposed F1 and F2 offspring post early life exposure to permethrin 10 microg/L", "GSE154206", "Other", "In the present study  zebrafish were exposed to permethrin during early life  and F1 and F2 generations were bred unexposed. Permethrin exposed F0 fish showed a hypoactive phenotype at maturity  whereas males from the F1 and F2 generations showed a decrease in anxiety like behavior. We performed transcriptomic analyses on whole brains GSE154020  and here  we further performed RRBS analyses to identify whether there was any stable change in DNA methylation that could be linked to the effects observed at other levels of organization. Due to technical issues during sequencing  we had to perform a correction on the raw data CombaT in order to remove a batch effect flow cell. We made sure that this did not create any false positive differentially methylated region. Processed files available are the results from methyl calling before batch correctionwith a min coverage >= 5 per C. A matrix of corrected data is available as supplementary file. Overall design: Reduced representative bisulfite sequencing was performed on males and females from the F0  F1 and F2 generations 4 replicates treatment  4 replicates control for each sex and each generation. Except only 3 treated male F0", null, "pubmed:33752003", null, "adult whole brain C13", "GSM4666878", null, "tissue:adult whole brain|strain:AB line|generation:F2|Sex:male", "adult whole brain C13", "Adaptor trimming with TrimGalore! Galaxy version 0.4.3.1 Alignment to GRCz11 with Bismark Galaxy version 0.22.1; optimizing alignement with \"L 0  0.6\". Rk due to batch effects described below  PE sequences were analyzed as SE. methyl calling using Bismark extractor  cov >= 5 processed data files batch correction using ComBat see supplementary data corrected matrix.csv identification of DMRs using Methylkit R v1.12; 300 bp tiles with at least 4 C included and >=10% differential methylation Genome build: DanRer11 Supplementary files format and content: methyl call cov >= 5 from bismark methyl extractor.  *.tabular files before correction and corrected matrix.csv post correction", "adult whole brain", null, "Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS", null, "strain:AB line|generation:F2|Sex:M", "GSM4666878", "GSM4666878: adult whole brain C13; Danio rerio; Bisulfite Seq", "GSM4666878", null, "1", "Fish were euthanized  brains were dissected and flash frozen in liquid nitrogen  and DNA was extracted using TriPrep extraction kit Macherey Nagel. 300 ng of DNA per sample were sent to the Environmental Epigenetics facility of IHPE  University of Perpignan  France  for pair ended or single ended RRBS", "GEO Accession:GSM4666878", "Bisulfite-Seq", "TRANSCRIPTOMIC", "Reduced Representation", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP271280", null, null, "P8-3_S30_L002_R1_001.fastq.gz", "fastq", 469628995.0, 2956090.0, "GSM4666878 r2", "0:158.87 1:0", "A:137163280;C:28944601;G:120359197;T:183126393;N:35524", 158, 0, null, null, 137163280, 28944601, 120359197, 183126393, 35524, "SRX8707732", "SRS6984319", "SRA1097340", "GEO", "UMR MARBEC, INRAE", 1, 0.00018, null, 0.00017, null, 1.0, null, null, null, 157, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "France", "2020-07-10", "Adult", "Adult", "Brain", "Nervous 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": ["60334"], "units": {}, "query_ms": 9.037072995852213}