{"database": "metadata", "table": "run_metadata", "rows": [[43769, "SRR6072787", "SRX3214261", "SRS2539118", "SRP118819", "PRJNA412050", "Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio", "GSE104221", "Other", "The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However  there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq  respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain  PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.", null, "pubmed:29686887", null, "PCB126 LIVER1 RNA Seq", "GSM2792787", null, "tissue:liver|treatment:PCB126|life history stage:Adult", "PCB126 LIVER1 RNA Seq", "Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.", "liver", "Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period  fish were reared in clean water for 7 days before sampling the tissues.", "Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.", null, "treatment:PCB126|life history stage:Adult", "GSM2792787", "GSM2792787: PCB126 LIVER1 RNA Seq; Danio rerio; RNA Seq", "GSM2792787", null, "1", "Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.", "GEO Accession:GSM2792787", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP118819", null, null, "PL1_S5_L001_R1_001.fastq.gz", "fastq", 1478813391.0, 28996341.0, "GSM2792787 r1", "0:51 1:0", "A:386520452;C:351444640;G:339630756;T:401202492;N:15051", 51, 0, null, null, 386520452, 351444640, 339630756, 401202492, 15051, "SRX3214261", "SRS2539118", "SRA612796", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.93711, null, 0.05155, null, 0.82528, null, 0.38533, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2017-09-25", "Adult", "Adult", "Liver", "Liver and Biliary 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": ["43769"], "units": {}, "query_ms": 10.590804000457865}