Fig. 5: Cell-to-cell variability in 3D genome features.

a, Merged scHi-C contact maps imputed by Higashi or predicted by the SBS model, as compared to bulk Hi-C and raw contact maps from scHi-C without imputation (top). Bottom left, insulation scores from bulk Hi-C, calculated after Higashi imputation, and SBS modelling. Bottom right, Spearman correlation coefficients between these contact maps. b, 3D models, raw scHi-C contact map, imputed maps from three similar cells between Higashi imputation and SBS model maps. The Higashi–SBS model contact map pairs have distance-stratified similarity scores of 0.69, 0.64 and 0.77 (left to right). c, The average normalized intensity of chromatin loops across 188 cells was calculated and compared by dividing loops on the basis of their position within TADs and A/B compartments (comp.). Left, the difference between loops in the same TAD (n = 181 cells) and loops spanning multiple TADs (n = 7 cells). Right, the difference between loops in the same A/B compartment (n = 157 cells) and loops spanning different compartments (n = 31 cells). A chromatin loop near RABGAP1L is highlighted in the right plot. The original distribution of the normalized intensity of this loop in each cell is shown in the right plots. Loops are stratified into groups depending on whether they locate within one TAD (n = 181 cells) or span TADs (n = 7 cells), or the A/B compartment state of loop anchors in each single cell (n = 15 (AA), n = 142 (BB) and n = 31 (AB) cells). The box plots show the median (centre line), IQR (box) and the whiskers extend to 1.5 × IQR. P values were calculated using two-sample two-sided t-tests. d, Aggregated contact map from single-cell Hi-C data at RABGAP1L (for cells with z score > 1.96). The circle with a dashed line indicates the 450-kb loop identified by SnapHi-C. e, Knight-Ruiz-normalized bulk Hi-C map from WTC-11 at RABGAP1L.