Identification of differentially DNA methylated regions. The fragmented genomes of macrophages (MAC) and immature dendritic cells (iDC) are separated into unmethylated (CpG) and methylated (mCpG) pools. Each pool is directly labeled using fluorescent dyes and each pool of one cell type is compared to the corresponding pool of the other cell type on a global promoter microarray. Microarray images are analyzed in combination to identify regions that show a reciprocal hybridization behavior. Representative scatter plots of CpG and mCpG pool hybridizations are shown. Probes enriched in the unmethylated pool of iDCs (red spots) were enriched in the methylated pool of macrophages (blue spots) and indicated the presence of DNA methylated regions. The reciprocal signal intensity ratios served as internal control for the reliability of microarray data.