Chromatin-associated RNA Profiling after EGF Stimulation

The cells were maintained in 0.5% FBS-containing medium for 48 h and then subjected to EGF stimulation for 20 min by adding 100 ng/mL EGF (Thermo Fisher Scientific, PHG0311L). For inhibitor treatment, the cells were incubated in medium containing 1 µM vemurafenib, 200 nM PD0325901, or 1 µM SCH772984 for 3 h before collection. The chromatin-associated RNA fraction was prepared as described previously (Lai et al. 2015 (link)). To prepare the samples for ChIP, the cells were fixed with 1% formaldehyde for 10 min in a culture dish followed by incubation in 0.125 M glycine at room temperature to halt the fixation. The cells were washed, scraped, and pelleted in cold PBS. ChIP was performed as described previously (Lai et al. 2015 (link)).