Given our findings where Th1 and Th17 cells influenced innate immune cell activation during craniotomy infection, scRNA-Seq was performed on CD45+ cells isolated from the brains of WT and Rag1–/– mice at days 3 and 7 after infection to obtain a more granular assessment of how innate responses are shaped in the presence or absence of lymphocyte subsets. Here, RAG1 is linked to infection.