Infinium EPIC Array-Based DNA Methylation Analysis

Array-based DNA methylation analyses were performed as previously described [7 (link)]. In brief, DNA was extracted by Qiagen Allprep DNA/RNA mini kit (Qiagen), concentration and quality of DNA were assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific), and 500 ng DNA was subjected to hybridization on an Infinium EPIC methylation array (Illumina, San Diego, CA; USA). The arrays were scanned, idat files were imported in R using the minfi package [20 (link)], and processed in accordance to the Illumina BeadStudio data analysis workflow (Illumina). Beta values were used for downstream hierarchical clustering analysis along with the beta values retrieved for glioblastoma samples from TCGA database https://www.cancer.gov/tcga [21 (link), 22 ].