Extended Data Fig. 8: Single-cell profiling of p53 mutant gastrointestinal tract.

a) Average log-transformed expression of the genes shown in Fig. 5a using published single-cell data^4,19. Cells were subdivided into emGut and exGut based on Rhox5 and Trap1a expression (see Methods). b) Bright-field microscopy images of a WT and a p53 KO E13.5 embryo, and the isolated gastrointestinal (GI) tracts (n = 4, one representative embryo is shown for each condition). No developmental phenotype is observed for the p53 KO embryo and GI tract compared to the WT. c) Average log-transformed expression of gastrointestinal epithelial marker genes in single cells corresponding to cell states annotated for WT and p53 KO embryos. d) Heatmap representation of the standardized, log-normalized expression levels of marker genes of cell states in E13.5 WT and p53 KO cells. e) Percentage of single cells assigned to the different cell states for each E13.5 WT and p53 KO single embryo replicate. f) Quantification of different read types spanning the Cas9 target sequences (g1 to g3) in WT and p53 KO cells. For the p53 KO cells, virtually no complete, error-free reads can be found implying the successful knockout of the target gene. g) Boxplot of prediction scores for p53 KO cells as they are assigned to their respective cell state based on the local neighbourhood of WT cells. The dashed line denotes the prediction score that reflects equal association with any of the nine cell states (random assignment). Lines denote the median, edges denote the IQR, whiskers denote 1.5 × IQR, and outliers are represented by dots (n = 4 biological replicates). h) Average log-transformed expression of the genes shown in Fig. 5a in the E13.5 WT and p53 KO cells. Cells were subdivided into emGut and exGut based on Rhox5 and Trap1a expression (see Methods).