Extended Data Fig. 4: Single cell analysis assigned known epidermal niches to cell clusters.
From: Tissue memory relies on stem cell priming in distal undamaged areas
a, UMAP of scRNA-seq replicates, relative to Fig. 3a–h and Fig. 4. b, Heatmap representing the 50 top marker genes for each cluster (left) and UMAP of cells coloured by the expression of selected genes (right). Top bars indicate the clusters and the time points. c, UMAP of cells coloured by assigned cell-cycle phase. d, Trajectories identified by pseudotime analysis. The starting points (black square) are Cluster 11 (JZ) for the upper HF and Cluster 5 (bulge) for the lower HF. e, Upper panel: plot of pseudotime trajectories and the associated heatmap with Smoothed Relative Expression (SRE). Lower panel: selected upregulated genes in the last cells of each trajectory are listed. Trajectory D is analysed alone in Fig. 4a, b. f, GO enriched for induced genes in the terminal clusters of each trajectory. Gene ratio (number of genes in the pseudotime/ number of genes in the GO term) and adjusted p-value (adjP) are plotted. g, UMAP of cells coloured by interscale and scale gene signature (left) and whisker plot of average z-score for scale and interscale gene groups in the epidermal terminal differentiation clusters (1, 2, 4, 12) of each trajectory (right). Gene signatures from Dekoninck et al. study27. n = 8 (IFE interscale), n = 9 (IFE scale) genes. h, Postn and Krt6a expressions are plotted on the UMAP. Scale in log(counts). i, GSEA ranking of the indicated gene signature using the differential gene expression estimated from the comparison 8w pw1 vs is 0w (upper panel) and 1w pw2 vs 1w pw1 (lower panel) in Transition Cluster. NES, normalized expression score. j, Violin plot of Krt6a expression in cells from Transition Cluster in each time point. Data are median with 25th and 75th percentiles. P-value (P) from a two-tailed t-test. scRNA-seq data (a-j) are the integration of two independent experiments, each of them based on 4 biological replicates.
