Fig. 1

S1 Hi–C protocol allows the generation of high-quality Hi–C maps. A Chromatin digestion and ligation of K562 cells and peripheral blood mononuclear cells. Lanes M show a 100 bp DNA ladder. 1 — intact gDNA, 2 — S1 digestion of cross-linked chromatin, 3 — ligation of S1-digested chromatin from lane 2. B Quality metrics of S1 Hi–C and DNase I Hi–C data sets. Each dot represents an independent Hi–C library preparation; we analyzed 14 DNase I Hi–C libraries [11] (protocol with biotin fill-in) and 16 S1 Hi–C libraries. P-values were calculated using the Mann–Whitney test. (∗ ∗) indicates p-value < 0.01, (ns) indicates p-value > 0.05. C Representative heatmap of chromatin interactions in K562 cells obtained using DNase I Hi–C protocol (below the diagonal line) [11] and S1 Hi–C protocol (above the diagonal line). D Genome-wide read coverage depth histograms. Each histogram shows distribution of coverage depth for 500 bp genomic windows. Data were obtained by merging all replicates E Boxplot showing coverage distribution similar to D, but for each replicate independently. Numbers near boxplots present quantification of interquartile range. F Boxplot showing distribution of Spearman’s correlation coefficient, calculated between pairs of Hi–C matrices for replicates. Numbers near boxplots represent median value