Alterations in RE accessibility during ESC differentiation. (A) Brightfield images of control (EGFP) or Oct4 KD ESC colonies indicate colony flattening and elongated cellular morphology upon Oct4 depletion. (B) Western blot of Oct4 in control (EGFP) or Oct4 KDs, indicating KD efficiency. RNA Polymerase II blot (Pol II) is shown as a loading control. (C, E) Average RE accessibility upon EGFP or Oct4 KD is shown relative to DHSs (C), or CTCF binding sites (E). (D, F) MNase-seq data. Nucleosome occupancy over DHSs (D), or CTCF binding sites (F). RED-seq and MNase-seq data are plotted as in Figure 3.