Fig. 4

Actively infected and uninfected ciliated cells are transcriptionally distinct from matched populations of survivor cells. a FACS gating strategy to isolate CD45- EpCam+ CD24+ (ciliated) cells from the lungs of Mock and Mal/04-Cre infected mice. Cre-activated tdTomato expression was used to identify 2 DPI infected and 14 DPI survivor cells. b Viral mRNA gene expression of the Mal/04 genome in 2 DPI infected and 14 DPI survivor cells (Normalized to 0 DPI). c Heatmap of the top 200 variably expressed genes across the four conditions (eight samples total) from murine lung ciliated cells: 0 DPI mock, 2 DPI actively infected with virus, 14 DPI tdTomato− uninfected and 14 DPI tdTomato+ survivor cells (14 DPI samples collected from the same lungs). Gene expression has been normalized using DeSeq2’s default scaling factor parameters and normalized using a shifted log transformation [log₂ (n + 1)]. Expression was then scaled across rows and the relative z-scores plotted. d Measurement of correlation distance between the indicated samples using Spearman’s rank test. e Heatmap of top 100 genes upregulated in 2 DPI cells compared to 0 DPI mock cells. Gene expression was then scaled across rows and the relative z-score plotted. f Gene Ontology of Biological Processes generated using DAVID software for genes differentially expressed between 14 DPI tdTomato− (uninfected cells) and 14 DPI tdTomato+ (survivor cells) red asterisks indicate GO processes that are associated with dysregulated cilia function or gene pathways not expected to be active in normal ciliated cells. g RNAseq gene expression, normalized to 0 DPI mock cells, for selected dysregulated genes derived from the pathways identified in the ontology analysis in f