Quantitative ChIP Assay for PDX1

ChIP was performed using the EZ-ChIP Kit (Millipore) according to the manufacturer’s protocol. Three batches of cadaveric human islets (250–300 IEQs) were used per experiment for each PDX1 immunoprecipitation. Insulinoma tissue was chopped into 2-3mm³ pieces and disassociated. Cells were counted using a hemocytometer. Chromatin was prepped from 250,000–300,000 cells according to the EZ-ChIP Kit protocol. The primer sets were designed based on the hypermethylated CpGs in insulinomas and PDX1 ChIP-seq peaks in whole human islets reported by Pasquali et al.^{16 (link)} and shown in Supplementary Fig. 10 (see Supplementary Data 14 for primer sequences). Immunoprecipitated DNA was quantified using ABI 7500 real-time quantitative PCR detection system (Life Technologies). The anti-PDX1 antiserum (AB2027) was kindly provided by Prof. Christopher Wright at Vanderbilt University and was diluted 1:100 for each ChIP experiment. Data are presented as fold-enrichment of the ChIP signal over the IgG signal.