up-regulated genes, there were previously reported AD associated genes, such as HTR2A, ANK3, BDNF, IL18, LRP8, MAPT, PPARα, SLC18A3 and VDR (david.abcc.ncifcrf.gov). In addition, we screened for the up-stream transcription factors for the differentially expressed genes, which might control aberrant gene expression in AD-NPCs (Supplementary Figure 4a). The enriched transcriptional factors that ranked on the top were mostly related to neuronal differentiation, apoptosis and neuroprotection.