ChIP-seq Data Analysis and Quantification

ChIP-seq data were obtained from GSM2104246 and GSM1571714 and were analyzed with WashU EpiGenome Browser (Washington University) to ascertain the binding site and the experimental design of ChIP-PCR^{29 (link),30 (link)}. According to the manufacturer’s protocol of the Magna ChIP HiSens Chromatin Immunoprecipitation kit (Millipore), 2 × 10⁶ cells were harvested in each ChIP reaction. Protein and DNA of each sample were crosslinked by applying 37% formaldehyde solution. SDS lysis buffer with protease/phosphatase inhibitor cocktail (CST, 1:100) was added after cell harvesting. After restriction enzyme digestion, centrifugation, and precipitation with beads, the precipitated DNA samples were quantified with specific primers via real-time PCR^{5 (link)}.