Suppl. Fig. S4). The sonicated DNA, diluted in TE buffer, was heat-denatured for 10 min at 95°C. 20 µl of DNA was removed and stored at −20°C and used as the input DNA sample. The remaining samples were incubated overnight with 5 µg of monoclonal mouse anti 5-methyl cytidine (Eurogentec, SanDiego, CA) in 5X IP Buffer. Then the DNA-antibody mixture was incubated for 2 hr with pre-washed Protein A agarose beads. The mixture was then washed, resuspended and incubated with Proteinase K overnight at 55°C. After phenol and chloroform extraction, DNA was precipitated with 70% ethanol and resuspended in 10 mM Tris-HCl. The final yield was 10–15 ng/µl. 10 ng of input DNA and immunoprecipitated DNA was amplified using Sigma WGA2 Genome Plex kit (Saint Louis, MO) and purified with a Qiaquick PCR purification kit (Qiagen, Fremont, CA). All the samples were further subjected to quality control analyses by the Nimblegen core facility (Reykjavik, Iceland) and were then labeled with Cy3 (input DNA) and Cy5 (immunoprecipitated DNA) dyes. Labeled input and immunoprecipitated samples were both hybridized to the same 2007-02-27_MM8_CpG island_promoter array (described below) as a two-color experiment and scanned using Nimblescan. The signal intensities for input DNA and immunoprecipitated
