Fig. 1

Cx3cr1^highCre⁻Eyfp⁻ microglia in Cx3cr1^{CreER-Eyfp/wt} mice. a Representative images of Hoechst, EYFP, Iba-1 and Tmem119 immunohistochemical staining in the brains of Cx3cr1^{CreER-Eyfp/wt} mice. White arrows point to the EYFP⁻Iba-1⁺Tmem119⁺ cells. Scale bar, 50 μm. b Comparison of morphology between EYFP⁺Iba-1⁺ microglia and EYFP⁻Iba-1⁺ microglia in Cx3cr1^{CreER-Eyfp/wt} mice. The graph shows process endpoints (left, p = 0.0773), process length (middle, p = 0.6047), and process occupied area (right, p = 0.1253) by Student’s two-tailed unpaired t test. n = 59 for EYFP⁺Iba-1⁺ cells and n = 31 for EYFP⁻Iba-1⁺ cells from four Cx3cr1^{CreER-Eyfp/wt} mice, mean ± s.d. C Representative dot plots of EYFP⁻ microglia in the brains of Cx3cr1^{CreER-Eyfp/wt} mice (gated as CD11b⁺CD45⁺Ly6C⁻ly6G⁻). d Representative dot plots of expression of EYFP and CX3CR1, n = 8. e Volcano plot showing the DEGs with FDR < 0.05, the indicated genes are Cx3cr1, all upregulated genes and the top 5 down-regulated genes. f The reads per kilobase of transcript, per million mapped reads (RPKM) of Cx3cr1 between EYFP⁻ and EYFP⁺ microglia from the RNA-seq data, p < 0.001 by paired Student’s two-tailed t test. g, h The RPKM of EYFP and Cre between EYFP⁻ and EYFP⁺ microglia from the RNA-seq data, **p < 0.01, ***p < 0.001 by paired Student’s two-tailed t test. I Dot plots of flow cytometry analysis of Cx3cr1^GFP/wt mice, values in plots are the ratio of GFP⁻ microglia to total microglia, n = 6 mice, mean ± s.d. j Representative images of GFP, Iba-1 and Tmem119 triple staining in Cx3cr1^GFP/wt mice, the arrows indicating cells expressing Hoechst, Iba-1, Tmem119, but not GFP, n = 6 mice. Scale bar, 50 μm