Fig. 4

Cell-type deconvolution reveals increase of ciliated cells in airways of old mice. a The multidimensional scaling (MDS) plot shows the mouse-wise euclidean distances of cell-type proportions for the two age groups. b The box plot shows the significant difference in the multidimensional scaling component 1 of cell-type proportions between young (n = 8) and old (n = 7). The box represents the interquartile range, the horizontal line in the box is the median, and the whiskers represent 1.5 times the interquartile range. c The Fruchterman–Reingold (FR) embedding of the airway epithelial cells in the dataset reveals distinct clusters of airway cell identity. d The indicated color code shows the distribution of young and old cells to the three clusters presented in (c). Note the increased density of old cells in the ciliated cell cluster. e The volcano plot shows negative log10 enrichment p values of cell-type marker signatures in the differential expression results of the bulk RNA-seq data from young and old mice. f The empirical density plot shows significant enrichment for ciliated cell-type marker genes (red line) compared to all other genes (black line) in the distribution of fold changes derived from the bulk differential expression analysis. g Club and ciliated cells were stained using a CC10 and Foxj1 antibody respectively (scale bar: 50 µm). h The boxplot depicts the quantification of ciliated cells from counting a total of 2647 club and ciliated cells in 14 individual airways of n = 2 mice of each indicated age group. i Ratio of ciliated to club cells in 14 individual airways of two mice for each indicated age group. The p values are derived from an unpaired, two-tailed t-test using Welch’s correction