Gene expression profiling in murine mononuclear phagocyte lineage cells

To understand the mechanism underlying monocyte and dendritic cell development through the regulation of Irf8 expression by the 56 kb downstream (+56 kb) Irf8 enhancer, we performed transcriptome analysis of bone marrow cells and splenocytes from wild-type, the Irf8 +56 kb enhancer-deficient, and IRF8-deficient mice. Taken together with the epigenetic profiling of mononuclear phagocyte lineage cells in these mice, the Irf8 +56 kb enhancer-mediated high Irf8 expression in hematopoietic progenitor cells promote type 1 classical dendritic cell (cDC1) differentiation, while low Irf8 expression in progenitors led to Ly6C+ monocyte development. RNA from murine hematopoietic stem cells (HSC), multipotent progenitors (MPP), granulocyte-monocyte progenitors (GMP), common dendritic cell progenitors (CDP), common monocyte progenitors (cMoPs), Ly6C+ monocytes (Mo), classical dendritic cells (cDC), and neutrophils (Neu) were isolated from wild-type, the +56 kb Irf8 enhancer-deficient (d+56kb), or IRF8-deficient (IRF8KO) mice was subjected to RNA-seq (biological duplicates for each cell type).