Figure 2

Comparison of RED-seq to naked DNA digestion. (A) RE accessibility reads from mouse ESC chromatin (top) and naked DNA (bottom) from a 3 Mb region of chromosome 14 (Chr14). Shown are normalized reads per million (RPM). (B) Scatterplot of RE accessibility [Log₂(RPM)] for Chr14 from chromatin relative to naked DNA. (C) RE accessibility from chromatin and naked DNA of two Hox genes, Hoxa4 and Hoxa11, which are silent in ESCs. Dotted lines highlight the genomic regions with RE accessibility differences apparent between chromatin and naked DNA. (D) RE accessibility from chromatin and naked DNA of two highly expressed genes in ESCs, Oct4 and Eef1a1.