The procedure for methylated DNA immunoprecipitation was adapted from previously published work,[47], [48], [49] and H3K9 acetylation ChIP assays[50] were performed using the ChIP assay kit protocol (06-599, Upstate Biotechnology), as previously described[6]. The amplification (Whole Genome Amplification kit, Sigma) and labeling reaction (CGH labeling kit, Invitrogen), and all the steps of hybridization, washing and scanning were performed following the Agilent protocol for chip-on-chip analysis (see Methods S1 for details). Three animals per group were used in the immunoprecipitation microarray experiments, and microarrays were hybridized in triplicate for each sample.
