Fig. 1: Steady-state and disease mouse mesothelial cell atlas.

a Schematic representation of the experimental procedure for the generation of the healthy state mouse mesothelial cell atlas. Thirty-two single cell datasets of healthy mouse mesothelial cells in twelve different organs were collected and integrated for the single-cell atlas generation. Preprocessed data and raw data were processed, annotated and then we extracted the mesothelial cells cluster based on the expression of Msln, Pdpn, Wt1 and the absence of Cd45, Cd34 and Epcam. Batch effect was then removed, and datasets were merged and analyzed. b UMAP embedding of 23,134 single cells in the steady-state atlas. The eight clusters identified through graph-based clustering are labeled with the most discriminative gene and indicated by different colors. c Hierarchical clustering of the different mesothelial cells, depending on the tissue of origin showing the hiearchy of the mesothelial cells in the different tissues. d UMAP embedding of 5,601 single cells in the mesothelial disease-state atlas. The three clusters identified through graph-based clustering are indicated by different colors. e UMAP embedding of the mesothelial disease-state atlas color coded with the expression of the highest enriched reactome terms. f Gene markers of the different disease states of the mesothelial cells. UMAP of mouse disease state mesothelial cell atlas, color coded for the different cluster markers. On the left bottom, is a heat map of the relative average expression, of the most strongly enriched genes for each cluster in the mesothelial disease state atlas (log(fold change), of one cluster versus all others. Created in BioRender. Kadri, S. (2025) https://BioRender.com/2qncy1b.