DNA Methylation Analysis via EPIC Beadchip

Bisulfite conversion of 500 ng DNA was performed with a EZ DNA Methylation^TM Kit (Zymo Research, Irvine, CA, USA), according to the manufacturer’s protocol. The genome-wide DNA methylation was assessed by the Infinium Human MethylationEPIC BeadChip platform (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. The microarray was scanned by the Illumina iScan system. The obtained data were further processed using the R language [46 ]. Quality control and data normalization were carried out in the minfi package as described previously [47 (link),48 (link)]. Raw data were converted into β values for further analysis [49 (link),50 (link)]. Probes mapped to single nucleotide polymorphism were removed from the analysis [51 (link)]. Differentially methylated probes were defined with |Δβ| > 0.2 (20% difference). The β value is defined as the ratio between methylated versus unmethylated alleles.