The data were accessed from the AMP-AD portal (synapse ID: syn7203233). This dataset comprises iPSC-derived microglia (n = 10) from human primitive streak-like cells [46]. Within 30 days of differentiation, myeloid progenitors co-expressing CD14 and CX3CR1 were generated. These iPSC-derived microglia were able to perform phagocytosis and elicit ADP-induced intracellular Ca2+ transients that asserted their microglia identity as opposed to macrophage. Single-ended RNA-seq data were generated with the Illumina HiSeq 2500 platform following the Illumina protocol.