Fig. 3: Fragment size and cross-linking affect compartment strength.
From: Systematic evaluation of chromosome conformation capture assays
a, Interactions (log transformed) for HFF cells obtained after cross-linking with FA only and digestion with MNase, DdeI, DpnII and HindIII, respectively. Principal component 1 (PC1) values of the genomic region are displayed below the figure. b, Saddle plots of genome-wide interaction maps for data shown in a. The signal of A–A and B–B compartmentalization in cis interactions become stronger with increasing fragment size. c, Quantification of the compartment strength using saddle plots of cis and trans interactions for 12 protocols applied to HFF cells, 9 protocols to non-synchronized HeLa-S3 (HeLa-S3 NS) NS, 12 protocols to DE cells, and 12 protocols to H1-hESCs. The y axis represents the strongest 20% of B–B interactions and the x axis represents the strongest 20% of A–A interactions, normalized by the bottom 20% of A–B interactions; that is, y = top(B–B)/bottom(A–B) and x = top(A–A)/bottom(A–B).
