Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain

Human brain organoid systems offer unprecedented opportunities to investigate both neurodevelopmental and neurological disease. Single cell-based transcriptomics or epigenomics have dissected the cellular and molecular heterogeneity in the brain organoids, revealing a complex organization. Similar but distinct protocols from different labs have been applied to generate brain organoids, providing a large resource to perform a comparative analysis of brain developmental processes. Here we take a systematic approach to compare the single cell transcriptomes of various human cortical brain organoids together with fetal brain to define the identity of specific cell types and differentiation routes in each method. Importantly, we identify unique developmental programs in each protocol, which will be a critical benchmark for the utility of human brain organoids in the future.