Fig. 4: Characterization of DTA+ cells and comparison to lung cells from COVID-19 patients. | Nature Communications

Fig. 4: Characterization of DTA+ cells and comparison to lung cells from COVID-19 patients.

From: Single-cell division tracing and transcriptomics reveal cell types and differentiation paths in the regenerating lung

Fig. 4

a Scheme of cell sorting and scRNA-seq strategy. Created with BioRender.com. b UMAP embedding showing epithelial cell type assignment before (day 0, n = 8 mice) and after tamoxifen administration (day 2, n = 10 mice). c Violin plot with normalized DTA expression in all epithelial cells. d Heatmap of the top five upregulated genes across epithelial cell types on day 2 ranked by power (roc test). Scaling of expression was done after downsampling to 100 cells per cell type. Black boxes highlight the expression of the marker genes of the closest epithelial population in DTA+ cells. e GSEA of common DEGs in DTA+ populations in relation to all non-DTA+ cells (MAST test, p_adj <0.05). The terms mentioned in the text are shown in bold. f Heatmap of the activities of 14 pathways inferred with PROGENY for all epithelial populations on day 2. g UMAP embedding showing cell type assignment of COVID-19 and control human epithelial cells integrated with SRC mouse epithelial cells (day 0 and day 2). Arrows point to DTA+-like cells present in the COVID-19 patient samples. h Heatmap of the top 40 DEGs in DTA+-like cells from COVID-19 epithelial cells. i GSEA of upregulated genes in the DTA+-like cells (MAST test, p_adj < 0.05). The terms in bold depict the clusters that are mentioned in the text.

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