Bulk RNA seq of intestinal immune cells from naïve, LCMV-Arm and LCMV-Cl13 infected mice

We report that the gastrointestinal tract (GIT) is a previously unappreciated long-term reservoir of chronic LCMV-Cl13 infection, and, chronic viral replication in the GIT has a profound effect on the local immune compartment as well as the development of subsequent immune responses. CD45+ immune cells were sorted and analyzed by RNAseq from the small and large intestines of naive mice, or mice infected 30 days prior with LCMV-Arm (acute virus) or LCMV-Cl13 (chronic virus). We show that GIT immune cells from acute and chronically infected mice differ substantially from naive mice; chronically infected mice show increases in genetic pathways involved in T cell activation and killing, inflammasome activation and interferon signaling; chronically infected mice show reduced expression of genes involved in T cell memory and antigen presenting cell activation; and chronic infection induces metabolic changes unique to the small but not large intestinal immune compartment. Overall design: 3 naïve, 3 LCMV-Armstrong (acute) infected and 3 LCMV-Cl13 (chronic) infected small (SI) and large (LI) intestinal samples of sorted CD45+ cells