Fig. 3

Repopulated EYFP⁻ microglia originate from the resident microglia pool. a Representative images of EYFP, Iba-1, P2ry12 triple staining on newly repopulated microglia of Cx3cr1^{CreER-Eyfp/wt}Rosa26^DTA/wt mice. Scale bar, 20 μm. b Experimental chimerism setup to determine the origin of repopulated Cx3cr1^highCre⁻Eyfp⁻ microglia after microglia depletion. Middle-left panel gated on CD11b⁺CD45⁺Ly6C⁻Ly6G⁻EYFP⁻ microglia. Middle-right panel with red color rectangle gated on F4/80^lowEYFP⁺ microglia. Bottom-left panel with blue color gated on F4/80^low EYFP⁻ microglia. Bottom-right with purple color gated on F4/80^high cells. n = 5–12, mean ± s.d. c, d Bar graphs show RPKM of Ms4a7 and Lyz2, n = 5, mean ± s.d. e Principal component analysis of genes p < 0.05. f Heat map visualization of specific genes on macrophage and microglia. Data is presented as mean-centered sigma-normalized