Gene expression changes in bone marrow dendritic cell progenitors upon acute and chronic LCMV infection [ATAC-seq]

Dendritic cell (DC) subsets are critical for immune responses, but their development from progenitors and maturation are often altered during infection, and the mechanisms underlying these changes remain unclear. To address this problem, we investigated the Chromatin landscapes of bone marrow DC progenitors from mice infected with lymphocytic choriomeningitis virus (LCMV). 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Armstrong 53b or Clone-13 or left uninfected. Bone marrow cells from 4-5 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in triplicates from uninfected control mice and infected mice at 8 days post infection and DC progenitors defined as Lin-c-Kitint/loFlt3+ cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, and CD8), NK cells (NK1.1), red blood cells (Ter119), granulocytes (Gr-1), and monocytes (CD11b)) were purified by using fluorescence-activated cell sorting (FACS). Samples were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol.