Early lung type I IFN response signature is higher in C57BL/6 than in susceptible C3HeB/FeJ mice. Bulk and single cell lung RNA-seq data were interrogated for expression of cytokine and cytokine response genes. (a) DESeq2-normalized expression values of the indicated cytokine genes in whole lung bulk RNA-seq data. (b) Dot plots showing expression of Tnf and Ifng in the indicated cell populations in scRNA-seq data. (c) DESeq2-normalized expression values of the indicated ISGs in whole lung bulk RNA-seq data. (d) Dot plots showing expression of individual representative ISGs or a 37-gene type I IFN response signature (Kotov et al., 2023) in myeloid cell populations in scRNA-seq data. Data shown in panels a and c are from a single bulk RNA-seq experiment with N = 5 mice per group. Points represent individual replicate mice as points with lines at the mean. Statistical analysis: two-way ANOVA with Holm–Sidak post hoc test: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, not significant. Data in panels b and d are from a single scRNA-seq experiment, and plots show combined data from cells from N = 3 mice per group. Circle sizes represent the abundance of cells expressing the gene, as a percentage of total cells. Circle color is proportional to the mean expression of the gene or signature within all cells in the cluster. See also Fig S4 and Fig. S5 a.