Protocol for generating and using human iPSC-derived microglia-containing air-liquid-interface cortical organoid cultures

Here, we present a protocol for generating long-term microglia-containing air-liquid-interface cortical organoid (MG-ALI-CO) cultures. This approach minimizes necrotic core formation, a common limitation of extended organoid cultures, favoring microglia survival and homeostasis. We describe steps for generating air-liquid-interface cortical organoids (ALI-COs), integrating macrophage precursors, and maintaining MG-ALI-COs. Additionally, we outline several experimental analyses of MG-ALI-COs, including immunostaining, imaging, and patch-clamp electrophysiological recordings. This model provides a physiologically relevant system to investigate human neuroimmune interactions in a 3D brain-like environment.