Myeloid–T cell chemokine interactions dominate lungs of C57BL/6 mice, while neutrophil recruitment is favored in TB-susceptible C3HeB/FeJ mice early during infection. Leukocyte clusters from our scRNA-seq dataset were subjected to CellChat analysis to infer cell–cell interactions, and expression of chemokine genes was examined in bulk and scRNA-seq data. (a) Circle plots showing predicted interaction strength between cell populations in the different conditions. Line colors indicate the inferred signal-sending population, line thickness is proportional to communication probability, and circle size is proportional to cell type/cluster abundance. (b) Bar plots showing the relative contribution of the indicated receptor/ligand pairs to total inferred interaction activity in each group. (c) DESeq2-normalized expression values of the indicated chemokine genes from bulk RNA-seq analysis of whole lung tissue. Points show individual replicate mice with lines at the mean. Statistical analysis: two-way ANOVA with Holm–Sidak post hoc test; *, P < 0.05; ***, P < 0.001; ****, P < 0.0001. (d) Dot plots showing expression of the indicated genes in myeloid cell populations in scRNA-seq data. 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 within all cells in the cluster. Data in panels a, b, and d are from a single scRNA-seq experiment, with plots showing combined data from cells from N = 3 mice per group. Data in panel c are from a single bulk RNA-seq experiment with N = 5 mice per group. See also Data S1 and Fig. S2.