Extended Data Fig. 1: Single-cell HiC approach to studying chromosome organization in mouse preimplantation embryos.

a, Distribution of total contact versus trans ratio per single blastomere, according to developmental stage with given thresholds for exclusion. b, Fraction of maternal contacts on the X chromosome versus contacts on the Y chromosome. The colour of each dot indicates the fraction of reads that cover the maternal genome. Red rectangles highlight female diploid cells, blue rectangles highlight male cells and black rectangles highlight haploid cells (that is, oocytes or polar bodies). Cells outside these frames were excluded. c, Percentage of short-range (25 kb–2 Mb) versus long-range or mitotic contacts (2–12 Mb) per single cell, coloured by developmental stages. d, Subset of the single cells at eight-cell stage, either in G1, S or G2 phase (top) or going towards mitosis (bottom), and their corresponding pseudo-bulk HiC heat maps. e, Table for the number of single blastomeres per stage of development that passed quality control, and the selected number after cell cycle phasing that were used to produce the subsequent analysis and heat maps. f, Bar plot of domain numbers for each developmental stage.