Extended Data Fig. 2: Cell cycle analysis and cluster connectivity.
a, Cell cycle analysis of epiblast cells from clusters 1, 3 and 4. Cell cycle phase was predicted with cyclone algorithm81 and shows that there are cells in S and G2M phase also in the loser and intermediate clusters. b, PAGA plot showing the connectivity of the five clusters of cells from CI-treated embryos. c-d, Diffusion map analysis in all epiblast cells (from DMSO and CI-treated embryos): cells are coloured according to the condition (c) and to the cluster (d). e, The pseudotime coordinate of the CI-treated epiblast cells obtained from the diffusion map including all epiblast cells correlates extremely well (with the pseudo-time coordinate obtained in the diffusion map calculated only from CI-treated epiblast cells (Fig. 2a). See methods for details on statistical analysis.
