IRF1 and infection: Indeed, the computed top DEG, typifying each cluster on day 3 in the effector phase of infection, hosted several interferon-induced anti-viral genes (Irf1, Irf7, Ifrd1, Socs1, Socs3, Ifit1, Bst2, and Isg15) as well as genes associated with mature resident Trm cells (Cd69, Nfkbid, Brd2, FosB) (Fig. 3b,e, Supplementary Fig. S5a and Data S2).