DNA was extracted from 1×106 cells (Qiagen DNeasy Blood and Tissue Kit), quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.), quality controlled (DNA1000 Kit and BioAnalyzer 2100, Agilent) and bisulfite-converted (EZ DNA Methylation Kit, Zymo Research) according to each manufacturer’s protocol. Bisulfite converted DNA was hybridized to Infinium HumanMethylation27K and Infinium 450K BeadChips (Illumina, Inc.), scanned with an iScan (Illumina, Inc.) and quality controlled in GenomeStudio. For 27K data, β values for each probe were range-scaled using data collected from DNA controls that were fully methylated (SSI DNA methyltransferase treated (NEB), bisulfite converted DNA), unmethylated (untreated genomic DNA) and half-methylated (50/50 mix of methylated and unmethylated controls). 450K data was background subtracted and normalized to controls in GenomeStudio. Hierarchical clustering was performed using Cluster, using Euclidian distance and complete linkage.
