To identify DMRs, DNA samples from untreated differentiated cells or undifferentiated cells, with or without ethanol treatment, were immunoprecipitated with 5mC antibody and labeled with Cy5. Input DNA was prepared and labeled with Cy3. Pairs of immunoprecipitated and input samples were mixed and hybridized to Nimblegen RN34 plus CpG island microarrays, designed to detect 19,530 rat promoters and CpG islands per slide. Each probed region is covered by ~50 nt oligos with ~50 bp gaps between them. The promoters and islands overlap 1.3 kb upstream and 0.5 kb downstream from transcription start sites for 21,632 RefSeq genes. Ratios of Cy5 to Cy3 indicate the relative enrichment of 5mC-immunoprecipitated DNA. Two approaches were taken to identify DMRs.
