Extended Data Fig. 3: Analysis on epiblast cells from DMSO and CI-treated embryos.
a, Heatmap showing the expression pattern of all genes differentially expressed along the trajectory from winning to losing cells in Fig. 2d. b-c, Overlap of genes differentially expressed along the trajectory joining winning and losing epiblast cells in CI-treated embryos (Fig. 2a and panel d) and genes targeted by p53. Pie charts show the percentage of genes up- or down-regulated in loser cells within the group of target genes that are activated (b) or repressed (c) by p53. There is an enrichment of activated/repressed targets among genes upregulated/downregulated in losing cells respectively (p-value=1E-4). The list of p53 targets is taken from58. d, Scatter plots of the expression levels of different marker genes plotted against each other in loser epiblast cells (cluster 4). Loser cells have higher expression of pluripotency markers as well as higher expression of some lineage-specific markers and the co-expression of these markers is only weakly correlated - the Spearman’s correlation coefficient is shown. e-g Our scRNA-seq data from epiblast cells is projected on top of previously published data from epiblast collected from freshly isolated embryos at different stages (E5.5, E6.25 and E6.5; data from26). First, a diffusion map (e) and a pseudotime coordinate (f) is computed for the epiblast cells from freshly isolated embryos. Then, a pseudotime coordinate is estimated for our data after projecting it onto the diffusion map. Panel g shows the pseudotime coordinates for both datasets, split by stage, treatment and cluster. See methods for details on statistical analysis.
