Extended Data Fig. 3: High-confidence consensus cell type markers, and cell-type-specific expression of asthma-associated genes.

a, Cell type clusters in full-length plate-based scRNA-seq data. Cell–cell Pearson correlation coefficient (r) between all 301 cells (individual rows and columns) ordered by cluster assignment (as in Extended Data Fig. 2d). Right, magnified view of 17 cells (black border on left) from the rare types. b, High confidence consensus markers. Relative expression level (row-wise Z score of mean log₂(TPM+1)) of consensus marker genes (rows, FDR <0.01 in both 3′-droplet and full-length plate-based scRNA-seq datasets; LRT) for each cell type (flanking colour bar) across 7,193 cells in the 3′ droplet data (columns, left) and the 301 cells in the plate-based dataset (columns, right). Top 15 markers shown, complete sets are in Extended Data Fig. 1f, Supplementary Table 3. c, Cluster-specific transcription factors in 3′ scRNA-seq data. Mean relative expression (row-wise Z score of mean log₂(TPM+1), colour bar) of the top transcription factors (rows) that are enriched (FDR <0.01, LRT, two-sided) in cells (columns) of each cluster. d–f, Cell-type-specific expression of genes associated with asthma by GWAS. d, Relative expression (Z score of mean log₂(TPM+1)) of genes that are associated with asthma in GWAS and enriched (FDR <0.01, LRT) for cell-type-specific expression in our 3′ scRNA-seq data. e, The significance (−log₁₀(FDR), Fisher’s combined P value, LRT) and effect size (point size, mean log₂(fold-change)) of cell-type-specific expression and its genetic association strength from GWAS¹⁵ for each gene from d. f, Distribution of expression levels (log₂(TPM+1)) in the cells in each cluster (x axis, colour legend) for two asthma GWAS genes: Cdhr3 (top; specific to ciliated cells) and Rgs13 (bottom; specific to tuft cells) FDRs, LRT.