Gene expression analysis of Mtb-infected mouse alveolar macrophages from mice lacking Nrf2 in LysM- or CD11c-expressing cells

The aim of this study was to measure the immune response of alveolar macrophages (AMs) from mice lacking Nrf2 in LysM- or CD11c-expressing cells to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing. Overall design: To characterize the early macrophage transcriptional response to Mtb infection, we infected mice with 2000-4000 CFU of mEmerald-H37Rv, and isolated AMs (CD45+, Zombie Violet-, CD3-/CD19-, Siglec-F+, CD11bmid, and CD64+) from BAL by fluorescence activated cell sorting at 24 hours following infection. Three populations were sorted for analysis by RNA-seq: Mtb-infected AMs (mEmerald+), bystander AMs (mEmerald-), and AMs from naïve mice.