Lung cytokine profiles are predominantly innate-derived in the primary and T cell–derived in the secondary response. (A) Differential expression of cytokine genes between the primary and secondary immune responses based on results from Fig. 1 (Padj ≤ 0.05, fold change ≤2) shown in a heatmap grouped by k-means clustering. Each column represents the average of four to five biological replicates for each condition and time point. Data are representative of two independent experiments. (B) Relative expression of cytokine genes (mean ± SD) that were more extensively upregulated in the primary (red) compared with secondary (blue) response over time after infection. Statistical significance was calculated by the Wald test using DeSeq2. (C) Similar to B showing relative expression of cytokine genes enriched in the secondary (blue) compared with primary (red) response. Graphs in B and C depict data from four to five biological replicates per condition and time point and are representative of two independent experiments. (D and E) Cytokine protein content in the BAL expressed as mean concentration ± SD grouped by those enriched in the (D) primary versus (E) secondary response compiled from two independent experiments (n = 7–13 mice per condition and time point). Statistical significance was determined by a two-way ANOVA. ****P ≤ 0.0001; ***P ≤ 0.001; **P ≤ 0.01; *P ≤ 0.05.