DNA methylation was assessed in mice using methods described previously17,18 using HpaII and HinP1I enzymes. Following quality control assessment through Agilent BioAnalyzer-based visualization, the unmethylated fraction of genomic DNA was hybridized to Affymetrix GeneChip Mouse Tiling Promoter 1.0R Arrays at the JHMI Deep Sequencing and Microarray Core facility (Baltimore, MD, USA). Affymetrix CEL files were background corrected and quantile normalized using the AffyTiling package in R, yielding normalized log2-transformed M values representative of the DNA hypomethylation profile per sample. Differentially methylated regions (DMRs) were calculated using the BioTile algorithm (http://psychiatry.igm.jhmi.edu/kaminsky/software.htm).19 Identified DMRs were refined by filtering out those not flanked within 1 kb of the DMR boundary by either an HpaII or HinP1I restriction site based on the mouse mm8 genome build sequence. Microarray data is located under GEO accession no.: GSE43460.
