Supplementary Figure 6: Unsupervised clustering of EMPs.

a, Heatmap showing scRNAseq expression within Lgr5-GFP + E14 subclusters including Lgr5 + EMP (n = 68) and stromal mesenchymal cells (n = 11). Marker genes are obtained from the scRNAseq data comparing LC (n = 73) to BC cells (n = 45) using SC3 with clustering parameter k = 2 and selecting marker genes with an AUC > 0.8 and a Wilcoxon signed rank test FDR adjusted p-value < 0.01. Expression of epithelial markers Krt14, Krt5 and Krt8 is also shown. The heatmap colouring represents the normalized expression in the scRNAseq where rows represent the top 27 marker genes for each cluster and columns represent EMP cells. b-e, Scatter plots depicting the correlation between the proportion of BC-specific (n = 53 cells) (b) and LC specific markers detected (n = 47 cells)(d) and total number of genes detected before (c) and after correction (e). Each dot (n = 193) represents a single cell, and colour represents cell type. Correction was performed using a robust linear model for each cell type using the rlm function in R, depicted for each population as a straight line with 95% confidence interval.