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

IFN-I suppresses the number of pre-pDCs and pDC development after 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) after IFN-I receptor blockade with neutralizing antibodies. 7 weeks old female C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Clone-13. C57BL/6J mice were intraperitoneally (i.p.) injected with 500ug/mouse of neutralizing antibody (nAb) against IFNAR or anti-mouse IgG1 isotype control on days -1 and 0 post LCMV Cl13-infecteion. Mice were then treated with 250ug/mouse anti-IFNAR nAb or isotype control i.p. on days 2,4, and 6 post-LCMV Cl13 infection. Bone marrow cells from 3-4 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in triplicates 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.