Fig. 1

Molecular heterogeneity of epidermal cells in culture. a Epidermal cell transcriptomes and cell state relation visualised using DDRTree and coloured according to unsupervised clustering. Each data point is one cell and axes are dimensionally reduced components of the cell transcriptomes. Colours and numbers represent the five identified cell states. b Gene expression for four marker genes shown for each cell on the state map. Top left: Integrin beta-1 (Itgb1), a basal IFE marker. Top right: S100 differentiation associated genes. Bottom left: Mt2, a basal IFE marker. Bottom right: Keratin 10, a suprabasal IFE marker of commitment to differentiation. c Barplot showing mean expression per cell averaged over all keratin associated messenger RNAs (mRNA) (top) and all collagen mRNAs (bottom). d Distribution of the expression of cluster-specific markers coloured according to cell state. Two markers are shown per cell state. Black line represents the median expression of the cluster. e Median expression of the top three markers for each state per cell on the state map. f Heatmap showing the similarity between epidermal cells from this study and IFE cells from Joost et al. Similarity is measured by Pearson’s correlation coefficient. Cells from this study are coloured by cluster along the vertical axis. Cells from Joost et al. are coloured by differentiation status along the horizontal axis. Joost et al. IFE cell legend is shown in order of differentiation status. B basal IFE cells, DI/DII differentiated suprabasal IFE cells, KI/KII keratinized IFE cells. g Heatmap showing similarity between cluster average transcriptomes from this study and proliferative IFE cells from Zhang et al. [14] and activated vs quiescent IFE cells from Lien et al. [15]