IFNA1 and infection: Although most of the perturbed transcripts within the IFN signaling (Fig 4D) and antigen presentation (Fig 4E) pathways were upregulated upon infection in both WT and Ifnar1-/- mice, some transcripts such as Ifng, Stat1, Tap1, Nlrc5 (Fig 4D and 4E) as well as other transcripts such as Il10 (S1 File) were expressed at a much reduced level in the infected WT compared to the infected Ifnar1-/- mice, suggesting that type I IFN signaling actually impairs the induction of these genes during infection.