These cells classified very close to wild-type microglia based on the expression of known markers (e.g. Cst3, Hexb), but displayed significant differences in gene expression of typical microglia homoeostatic genes (e.g. P2ry12/P2ry13, Cx3cr1, Tmem1), known AD risk factors (e.g. ApoE, Lpl, CD9, Ctsd, Tyrobp, Trem2), and other genes involved in lipid metabolism and phagocytosis (e.g. Lpl, Cst7). Here, TREM2 is linked to Alzheimer disease.