biostudies-literatureUzquiano ABroad Institute Klarman Cell ObservatoryHoward Hughes Medical InstituteNIMH NIH HHSBroad Institute Stanley Center for Psychiatric ResearchNational Institutes of HealthHarvard UniversityChan Zuckerberg InitiativeBroad Institute3770-3788.e27https://www.ebi.ac.uk/biostudies/studies/S-EPMC9990683biostudies-literatureUnknown185(20)Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell typeCellProper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex.PMC9990683U01 MH115727R01MH112940P50MH094271RF1 MH123977U01MH115727R01 MH112940P50 MH094271RF1MH123977Kedaigle AJJin XBuenrostro JKim KGerhardinger CChen FLevin JZPaulsen BAdiconis XVelasco SAnton-Bolanos NNagaraja SArlotta PMurray ERegev APigoni MUzquiano AFaits TTucewicz AfalseProper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex.Realizing the full utility of brain organoids to study human development requires understanding whether organoids precisely replicate endogenous cellular and molecular events, particularly since acquisition of cell identity in organoids can be impaired by abnormal metabolic states. We present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, from generation of neural progenitors through production of differentiated neuronal and glial subtypes. We show that processes of cellular diversification correlate closely to endogenous ones, irrespective of metabolic state, empowering the use of this atlas to study human fate specification. We define longitudinal molecular trajectories of cortical cell type2022-01-01T00:00:00Z2022 Sep2025-08-23T03:09:03.236Z2025-02-18T23:48:06.626ZS-EPMC99906833617966910.1016/j.cell.2022.09.010