Infinium Methylation EPIC BeadChip Analysis

Following bisulfite treatment of 1 μg genomic DNA using the EZ DNA Methylation kit (Zymo Research, Irvine, CA), the bisulfite-converted DNA was hybridized onto the Infinium Methylation EPIC BeadChip (Illumina, San Diego, CA), following the Illumina Infinium HD Methylation protocol in the Genomics Core Facility at UAMS. The Methylation EPIC BeadChip covers over 850,000 CpG sites, and has increased genome coverage of regulatory regions and higher reproducibility and reliability compared to previous versions [3 (link)]. Whole genome amplification, hybridization, staining and scanning steps for all samples were performed, the Illumina iScan SQ scanner was used to create images of the single arrays, and the intensities of the images were extracted using the Methylation module (v.1.9.0) of the GenomeStudio (v.2011.1) software (Illumina). Raw intensity data as IDAT files were imported into GenomeStudio for the computation of detection p-value of the probes, and all further steps including data import, normalization, filtering and analyses were performed using the methylation pipeline in Partek Genomics Suite^™ 6.6 (Partek Inc., St. Louis, MO).