with the use of ligation-mediated PCR (Sikder et al., 2006). Cy5-labeled immunoprecipitated DNA and Cy3-labeled total DNA were mixed and hybridized to MM8 NimbleGen promoter microarrays (Madison, WI), which span the promoters of ~20,000 genes. After pre-processing, normalization, and identification of binding sites using Mpeak, statistical analysis of cocaine-induced changes in promoter occupancy was performed. Since the distribution of fold changes was slightly short-tailed, we performed a non-parametric analysis using 3.1 standard deviations as a cutoff, which would roughly correspond to p < 0.001 under normal assumptions (see Supplemental Methods). These unique datasets provided a novel view of cocaine-regulated gene targets and the regulatory mechanisms in this critical brain reward region.
