(A, C, E, G, H, J) Representative flow cytometry histograms and quantitation of AF subset frequency and/or AF signal intensity in AF+ microglia isolated from mice of indicated genotypes. Significance established with unpaired Student’s t-test (A, C, E, G), 2-way repeated measures ANOVA followed by Sidak’s post-hoc (H), and 1-way ANOVA followed by Tukey’s post-hoc (J). (B, D, F, I, K) Quantitation of LAMP1 levels in microglia isolated from mice of indicated genotypes, calculated as net geometric mean fluorescence intensity after subtraction of background AF signal and normalization to AF intensity detected in AF− microglia from wild-type age-matched control mice. Significance established with unpaired Student’s t-test (B, D, F, I) and 1-way ANOVA followed by Tukey’s post-hoc (K). n ≥ 6 animals per genotype group from at least two independent experiments. All groups were age-matched and all data presented as mean ± SD. AF = autofluorescence; B = blue laser; YG = yellow green laser; ns = not significant, *p<0.05, **p<0.01, ***p<0.001. See also Figure 6—figure supplements 1 and 2.