{"database": "metadata", "table": "run_metadata", "rows": [[67570, "SRR17210877", "SRX13390796", "SRS11294330", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep2", "GSM5730178", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730178", "GSM5730178: RNAseq DMSO Rep2; Danio rerio; RNA Seq", "GSM5730178", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730178", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T3_S2_R1_001.fastq.gz", "fastq", 1756085856.0, 34433056.0, "GSM5730178 r1", "0:51 1:0", "A:409690032;C:438746739;G:419437935;T:488094432;N:116718", 51, 0, null, null, 409690032, 438746739, 419437935, 488094432, 116718, "SRX13390796", "SRS11294330", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95577, null, 0.06639, null, 0.64076, null, 0.49674, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive 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": ["67570"], "units": {}, "query_ms": 12.697968006250449}