Extended Data Fig. 3: Dynamics of domains in single cells.

a, Distribution of the minimal distance between cluster centroids (D_min) for a predefined number of clusters (k) ranging from 2 to 40. Clustering was performed 100 times for each value of k. The optimal number of clusters is the highest value of k before the value D_min becomes stagnant. b, Heat maps representing the result of clustering for different values of k. The same main categories are found for k > 8. The contact enrichment colour scale corresponds to the maternal (red) and paternal (blue) heat maps; the differential contact enrichment scale corresponds to the differential (maternal − paternal) heat maps. c, Heat maps showing ___domain enrichment in the bulk HiC data from GSE82185, with the same order as our clustering in Fig. 1d and showing similar dynamics. d, Single-cell projection by UMAP from the quantification of ___domain contacts on each allele, using all cells and all chromosomes, coloured by stage (top) or by sex (bottom). n = 669 single cells. e, As in d but excluding domains on the X chromosome. f, As in e but coloured by cell cycle phasing. g, Cell cycle phasing based on short-range versus mitotic contacts, with the same colour scale as in f. h, Single-cell projections after excluding oocytes, all cells in pre-M and M phase and domains on the X chromosome, as in Fig. 1f, coloured by sex (top) or by pseudotime overlaid with the inferred trajectory (bottom). n = 470 single cells. i, As in h, coloured by mean count per kb per million (CPKM) on each allele, for the nine clusters identified in Fig. 1d.