ChIP was carried out following standard protocols. Briefly, 4-million cells were fixed with 1% formaldehyde for 10 min and sonicated on ice at 40% amplitude (30 s on, 90 s off, for a total of 24 min) using a Branson 101-135-126 Sonifier. ChIP was performed using 5 μl of a polyclonal anti-CTCF antibody (Millipore 07–729), 10 μl monoclonal anti-CSB antibody (1B1) (9 (link)) and 5 μl recombinant protein-G agarose beads (Invitrogen). ChIPed DNA was analyzed by real-time PCR using a 7900HT Fast Real-Time PCR System from Applied Biosystems and SYBR green. Primers were as described in Supplementary Table S7. For all ChIP-qPCR experiments described in this manuscript, menadione treated and untreated cells were examined side-by-side. For the ChIP-seq experiments, the CSB+M sample was processed alongside one untreated sample, which was previously reported (9 (link)).
For western blot analyses, ChIP samples were reverse cross-linked in SDS sample buffer at 95°C for 30 min (8 (link)).
For western blot analyses, ChIP samples were reverse cross-linked in SDS sample buffer at 95°C for 30 min (8 (link)).
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