ChIP-qPCR Analysis of Transcription Factors

ChIP was performed using standard protocols (38 (link)) on >1 × 10⁶ cells per immunoprecipitation, with an SMC1A antibody (Bethyl Labs, catalog # A300–055A), a Med1 antibody (Bethyl Labs, catalog # A300–793A), an RNAPII antibody (Millipore, catalog # 05–623) and a phospho-IRF3 antibody (Cell Signaling, catalog # 4947). See Supplementary Table S1 for primer sequences, designed with Primer 3 (39 (link)). Real-time PCR was performed as described above (see 3C), using 500 pg of ChIP DNA per reaction. If the starting sample size was ≥5, and the removal of a single data point reduced the standard error by over 20%, that data point was excluded as an ‘outlier.’ In these instances, no more than one data point was removed.