Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex

Stem cell-derived human brain organoids hold an unprecedented degree of promise as experimental models of the human brain. They are, however, plagued by poor reproducibility and high organoid-to-organoid variability. Here, we show that a human organoid model pre-patterned to form the dorsal forebrain and cultured for over six months can achieve reproducible generation of a rich diversity of cell types appropriate for the human cerebral cortex. Using single-cell RNA-sequencing of 166,242 cells isolated from 21 individual organoids, we find that 95% of the organoids generated a virtually indistinguishable compendium of cell types, through the same temporal trajectories, and with organoid-to-organoid variability that is comparable to that of individual endogenous brains. The data demonstrate that reproducible development of complex central nervous system (CNS) cellular diversity does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments. Overall design: Single cell RNA-sequencing from 21 individual organoids, after 3 or 6 months in culture. Batches of 3 organoids from each differentiation. Position-sorted BAM files as created by CellRanger v.2.0.1 are supplied to SRA as raw data files. Each read has Chromium cellular and molecular barcodes information stored as TAG fields.