fragment sizes between 200-1000 bp (verified on 2% agarose gel). A 25 μl of sonicated DNA from each sample was kept as Input DNA and the rest of the 100μl was used for Immunoprecipitation with 5-methylcytosine antibody using a Methyl capture kit (Epigentek, Brooklyn, NY). The 10ng of input DNA and immunoprecipitated DNA was amplified using a Sigma WGA2 Genome Plex kit (Saint Louis, MO) and purified with Qiaquick PCR purification kit (Qiagen, Fremont, CA). All samples were further subjected to quality control analyses by the Nimblegen core facility (Reykjavik, Iceland) and then labeled with Cy3 (input DNA) and Cy5 (immunoprecipitated DNA) dyes. Labeled input and immunoprecipitated samples were both hybridized to the same RN34 Promoter plus CpG island microarray (described below) as a two-color experiment and scanned using Nimblescan. The signal intensities for input DNA and immunoprecipitated DNA were used to calculate the ratio of IP/Input DNA.
