DIG-seq using native chromatin DNA. (A) Overview of DIG-seq to identify genome-wide Cas9 in vitro cleavage sites using native chromatin DNA. (B) A representative IGV image showing a staggered alignment (top) and a straight alignment (bottom) of whole-genome sequence reads at the on-target site. (C) A Venn diagram showing the number of in vitro cleavage sites identified by Digenome-seq using histone-free DNA or by DIG-seq using chromatin DNA with the HBB-targeted CRISPR-Cas9. (D) Sequence logos obtained via WebLogo using in vitro cleavage sites captured by Digenome-seq or DIG-seq. (E) Scatterplot of DNA cleavage scores at sites captured by Digenome-seq versus DIG-seq. (F) Scatterplot of indel frequencies versus DNA cleavage scores at sites captured by DIG-seq using HeLa chromatin DNA. (G) Pearson's correlation coefficients (R-square values) obtained with indel frequencies versus DNA cleavage scores at off-target sites identified by Digenome-seq using chromatin or histone-free DNA. Error bars, SEM (n = 5). The P-value was calculated by Student's t-test.
