Fig. 3

Differential reprogramming of RNA populations by viral and bacterial infection. Using RNA from the same total RNA samples as used for small RNA sequencing (Fig. 2), long RNA populations were determined by RNAseq 24 h after infection or mock treatment (n = 5 per condition). A PCA indicating somewhat better separation than with sncRNAseq (compare Fig. 2E). B Venn diagram showing the number of DE mRNAs (pAdj ≤ 0.1, FC ≥|2| with respect to uninfected tissue) unique to each pathogen, shared between any two pathogens, or common to all three. C–H Volcano plots identifying DE mRNA and lncRNA species with respect to uninfected tissue in infection with IAV (C–E), BCG (F), and P. aeruginosa (G), and comparing P. aeruginosa vs. BCG infected HLTEs (H). Cutoffs were set at FC =|2| (i.e. log₂ =|1|) and p-Adj 0.1 (i.e. − log₁₀ = 1)