After ChIP, the immunoprecipitated DNA was pre-amplified with a whole-genome amplification kit (Sigma #WGA2) following the manufacturer’s protocol, and 2 μg DNA was labeled using a SureTag complete DNA labeling kit (Agilent Technologies #51904240) at 37 °C for 2 h then 65 °C for 10 min. Input DNA was then labeled with cyanine 3 while immunoprecipitated DNA was labeled with cyanine 5. Both samples were purified on columns and eluted in TE buffer. Labeled DNAs were mixed and competitively hybridized to DNA microarrays. Hybridization was carried out on 2X400K Sure Print G3 Human promoter microarrays (Agilent #G4874A) in the presence of human Cot-1 DNA for 40 h at 65 °C and the slides were washed according to Agilent’s procedure. After washing, the slides were scanned using an Agilent microarray scanner, and intensity of fluorescent signals was extracted using Agilent feature extraction 11.2 software.