AIF1 and Alzheimer disease: Given that the set of genes that define the IBA1+CD74high microglial cells of cluster 7 are enriched in AD-related genes (Fig. 8b) as well as the DAM signature (Fig. 6b) and that this gene set is downregulated in the cortex of individuals with a diagnosis of AD (Fig. 8c), we expanded our in situ study to include 8 cases of AD dementia that also fulfill a diagnosis of pathologic AD and 11 subjects that meet neither of these diagnostic criteria; all subjects underwent autopsy at the New York Brain Bank and were characterized in the same, structured manner (Supplementary Data 9).