Fig. 5

Characterization of hPSC-derived cortical excitatory neurons by scRNA-seq. a tSNE projection of 4857 single-cell transcriptomes of hPSC-derived neuronal cell types after 86 days of differentiation. Unsupervised clustering using MCL groups cells into four major classes: Neurons (N), neuroepithelial progenitors (NP), mixed glial cells (G), and Cajal-Retzius cells (CR). In addition, a small population of fibroblasts (Fib) is identified. b The identified cell populations are characterized by expression of known markers for the expected cell types. Expression values are shown as log2 (normalized UMI counts + 1). c tSNE projection, colored by CellSIUS assignment. Main clusters are denoted .main, subclusters .sub. d Mean expression of each marker gene set identified by CellSIUS, projected onto the same tSNE map as shown in a. The top markers are indicated for each gene sets; numbers in brackets refer to how many additional genes are part of the marker gene set. e Comparison of the gene signature uncovered by CellSIUS to genes found to be enriched (p < 0.05) in choroid plexus of the fourth ventricle according to harmonizome [47, 48]. f Single optical sections of neurosphere cryosections acquired by confocal microscopy showing co-localization of TTR and PTGDS in cells predominantly on the periphery of neurospheres (panel left—composite image of a neurosphere; panels right—split images from a different neurosphere)