Cells were harvested and MEFs depleted from ESC cultures. ESCs and NSCs were crosslinked in 1% formaldehyde for 10 minutes at room temperature. ChIP was carried out as described in Illingworth et al. (2015). Briefly, cells were lysed and sonicated to an average fragment length of 250bp using a Qsonica. Chromatin was incubated with protein A dynabeads pre-bound with antibody overnight at 4C. Beads were washed and DNA eluted. Sequencing libraries were prepared as described in Bowman et al. (Bowman et al., 2013).