Extended Data Fig. 1: Identifying tracheal epithelial cell types in 3′ scRNA-seq.

a, Quality metrics for the initial droplet-based 3′ scRNA-seq data. Distributions of the number of reads per cell (left), the number of the genes detected with non-zero transcript counts per cell (centre), and the fraction of reads mapping to the mm10 transcriptome per cell (right). Dashed line, median; blue line, kernel density estimate. b, Cell type clusters are composed of cells from multiple biological replicates. Fraction of cells in each cluster that originate from a given biological replicate (n = 6 mice). Post hoc annotation and number of cells are indicated above each pie chart. All biological replicates contribute to all clusters (except for wild-type mouse 1, which did not contain any of the very rare ionocytes (0.39% of all epithelial cells)), and no significant batch effect was observed. c, Reproducibility between biological replicates. Average gene expression values (log₂(TPM+1)) across all cells of two representative 3′ scRNA-seq replicate experiments (r = Pearson correlation coefficient). Blue shading, gene (point) density. d, Post hoc cluster interpretation based on the expression of known cell type markers. t-SNE of 7,193 scRNA-seq profiles (points), coloured by cluster assignment (top left), by expression (log₂(TPM+1)) of single marker genes, or by mean expression of several marker genes⁴ for a particular cell type. e, Cell type clusters. Pearson correlation coefficients (r, colour bar) between every pair of 7,193 cells (rows and columns) ordered by cluster assignment. Inset (right), zoom of 288 cells from the rare types. f, Gene signatures. Relative expression level (row-wise Z score of log₂(TPM+1) expression values) of cell-type-specific genes (rows) in each epithelial cell (columns). Large clusters (basal, club) are down-sampled to 500 cells.