snRNA-Seq data of human iPSC-midbrain organoids without and with microglia

The human brain is a complex, three-dimensional structure. To better recapitulate the brain complexity, recent efforts focused on the development of human specific midbrain organoids. Midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astroglia and oligodendrocytes. However, the absence of microglia, with their ability to phagocyte apoptotic cells and debris represents a major disadvantage for the midbrain organoid system. Additionally, neuro-inflammation-related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of iPSC-derived microglia in brain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into midbrain organoids. Using single nuclear RNA sequencing in collaboration with the RIKEN institute we provide a detailed characterization of the microglia in brain organoids as well as of the influence their presence has on the other cells of the organoids. We generated human midbrain organoids from a wild-type (WT) iPSC line. At day 15 of differentiation, we co-cultured them with human iPSC-macrophage precursors generated from three different WT lines and promoted microglia differentiation in 3D. After 20 days of co-culture, we snap-froze the organoids and proceeded to single nuclei RNA seq to see differences in gene expression coming from the presence or absence of microglia in the system.