Methylation of individual CpGs was derived by observing bisulfite conversion of unmethylated cytosines in RRBS reads when compared to the reference genome. Methylation maps of individual CpGs show the average methylation value obtained by dividing the number of reads on which the CpG was methylated by the total times the CpG was covered by a read. Promoters were defined as 1 Kb up- and downstream of Refseq gene transcription start sites. Methylation values of individual CpGs in promoters were pooled in a weighted manner (i.e. proportional to the number of reads covering that CpG).
