Fig. 5: Single-cell RNA sequencing.
From: Club cells employ regeneration mechanisms during lung tumorigenesis
a Experimental strategy of scRNA sequencing analysis. b UMAP of the high-quality cells. Cells are coloured by the clusters identified using a shared nearest neighbour (SNN) modularity optimization-based clustering. c UMAP embedding showing the distribution of the cells collected from the different time points. Coloured dots represent the cells collected at the indicated time point; grey dots represent cells from the other time points. d Percentage of cells in each cluster, coloured by sample origin. The relative contributions were normalized to the number of cells in each sample. e UMAP coloured by the cell-type annotation of the study set. The annotation combines previously published cell-type-specific markers42, 46 and manual curation and is based on the most significant marker genes of each cluster or cell group (Supplementary Table 5). f UMAP with cells coloured by expression of Club (Scgb1a1, Scgb3a2), AT2 (Sftpc, Lyz2) and AT1 (Hopx, Ager) cell-type-specific markers. Colours represent the normalized expression levels for each marker in each cell. g Violin plot depicting the normalized expression of Alk by cluster indicating elevated expression in clusters 11, 12, 13 and 14. h Cell-type composition of each collected sample.
