Abstract: Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to study human brain development, evolution and disease. However, it is unclear which parts of the human brain are covered by existing protocols, and it has been difficult to quantitatively assess organoid variation and fidelity. We integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated human neural organoid cell atlas totalling more than 1.7 million cells. Mapping to developing human brain references shows primary cell types and states that have been generated in vitro, and estimates transcriptomic similarity between primary and organoid counterparts across protocols. We provide a programmatic interface to browse the atlas and query new datasets, and show that the atlas can be used as a diverse control cohort to annotate and compare organoid models of neural disease, identifying genes and pathways that may underlie pathological mechanisms with the neural models. We also find that the posterior brain regions are generally underrepresented and understudied in the brain organoid community, and therefore perform single-cell multi-omic and spatial characterization of posterior brain organoid development. We perform gene regulatory network inference and transcription factor perturbation which resolve mechanisms underlying neuronal differentiation. We perform multiplexed patterning screens, and identify morphogen concentration and combinations that expand existing organoid models.
