Fig 1: IBV survivor cell populations are predominantly composed of cells expressing ciliated cell markers. a Tracheas were collected from Mock and Mal/04-Cre infected mice at 2 and 14 DPI then opened longitudinally and flattened to image the surface area of the whole-mount tracheal epithelium. Scale bar = 25 µm. b Quantification of apical surface area covered by tdTomato+ survivor cells from whole-mount trachea images. n = 4, 12 images per group, respectively, Student’s T-test. c Flow cytometry of 14 DPI tdTomato- (uninfected cells) and 14 DPI tdTomato+ (survivor cells) from the lungs of Mal/04-Cre infected mice, where cells are stained with CD24 (ciliated), SSEA-1 (secretory), GSIB4 (basal) cell surface markers. d Quantification of flow cytometry. n = 3 mice per group. e Cross-sectioned microscopy of murine tracheal epithelial cells from mice 14 days post-infection with Mal/04-Cre stained with KRT5 to label basal stem cells and SSEA-1 to label secretory cells. f Cross-sectioned microscopy of murine tracheal epithelial cells from mice 14 days post-infection with Mal/04-Cre stained with FOXJ1 to label ciliated cells. g Quantification of tdTomato+ survivor cells stained with cell-specific markers: KRT5, SSEA-1, and FOXJ1 compiled from two independent experiments. Data are presented as the number of marker+ cells out of total tdTomato+ cells and the percentage was calculated for marker+ cells out of total tdTomato+ cells imaged. S.E.M was plotted to indicate variability around the mean for tested samples, *p = 0.05, **p = 0.001, ns not significant