Figure 1

Experimental and bioinformatics pipeline. Next generation sequencing was performed after methylation-sensitive enzyme-based enrichment using the Illumina Genome Analyzer IIx (GAIIx) platform with single-end read length of 80 bp on 12 genomic liver DNA samples obtained from isogenic day 22 a/a mice, exposed to BPA through maternal dietary intake (control, 50 ug/kg diet, or 50 mg/kg diet; n = 4 per group). To regions of altered methylation (RAMs) associated with BPA exposure group, the number of aligned sequencing reads per 100 bp window with 50 bp moving shifts was obtained for each sample. edgeR analysis was performed after applying filters to remove the regions with low reads. Top candidates were identified, and candidate RAMs were validated using EpiTYPER.