Mouse data, probe, and intensity data for each sample were imported into R using the package RnBeads (version 2.10.0), followed by preprocessing to filter probes outside the CpG context, SNP probes, sex chromosome probes, probes without intensity value, and probes with a low standard deviation. The RnBeads.mm10 package was used to annotate the location of each probe. Downstream data analysis was performed using β values. The β value is the ratio of the methylated probe intensity to the overall intensity (the sum of the methylated and unmethylated probe intensities). βvalues range from 0 to 1, in which 0 is no methylation and 1 is complete methylation and were used to derive heatmaps and further analysis. Differential methylation between groups was defined as β value difference and adjusted p-value (Benjamini-Hochberg method, FDR <0.05).
