We performed RNA sequencing on 40,000 cells to create a high-resolution
single-cell gene expres-sion atlas of developing human cortex, providing the
first single-cell characterization of previously uncharacterized cell types,
including human sub-plate neurons, comparisons with bulk tissue, and systematic
analyses of technical factors. These data permit deconvolution of regulatory
networks connecting regulatory elements and transcriptional drivers to
single-cell gene expression programs, significantly extending our understanding
of human neurogenesis, cortical evolution, and the cellular basis of
neuropsychiatric disease. We tie cell-cycle progression with early cell fate
decisions during neurogenesis, demonstrating that differentiation occurs on a
transcriptomic continuum; rather than only expressing a few transcription
factors that drive cell fates, differentiating cells express broad, mixed
cell-type transcriptomes before telophase. By mapping neuropsychiatric disease
genes to cell types, we implicate dysregulation of specific cell types in ASD,
ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access
and browsing. An extensive single-cell catalog of cell types in the mid-gestation
human
neocortex extends our understanding of early cortical development, including
subplate neuron transcriptomes, cell type specific regulatory networks, brain
evolution and the cellular basis of neuropsychiatric disease.