Fig. 2

Repopulated microglia-like cells after depletion and WBRT originate from peripheral monocytes and retain monocytic signatures. a Experimental design of head-protected bone marrow transplantation (BMT) followed by CSF-1Ri-mediated microglia depletion and WBRT. Lower panel shows fur colors before euthanasia for brain analysis. b Representative FACS analysis gating strategy to analyze bone marrow chimera efficiency 6 weeks after BMT, about two-thirds of the CD11b⁺Ly6C^high monocytes are replaced by GFP⁺RFP⁺ cells derived from donor bone marrow cells. c Representative FACS analysis gating strategy and brain myeloid composition results. Upper panel shows FACS gating using CD45 and CD11b staining; microglia and microglia-like cells are defined by positive CD11b staining and low or intermediate CD45 levels. Lower panel shows scatter plots of GFP/RFP fluorescent levels of the CD11b⁺CD45^{low/intermediate} population in the brain, and a dot plot comparing percentages of peripheral myeloid cell derived microglia-like cells. Statistical analysis was performed using unpaired t-test, ***p < 0.001. d Hierarchically clustered heatmaps to compare microglia and monocyte signatures. A signature gene list was defined using a dataset published by Lavin and Winter et al., GSE63340. Defined list and expression details are in Additional file 3: Table S2. e Similarity matrix comparisons using defined monocyte and microglia signature genes. f Bar graph showing similarity scores to compare relative numbers of genes (in percentage of the defined list) that express in the same trends as monocytes or microglia based on the Lavin and Winter et al. dataset