Fig. 4

Protocol-dependent differences in transcriptomic profiles in neuronal cell populations. A Percentage of neuronal subtypes in each sample. B Changes in expression levels of genes characteristic of dorsoventral development along pseudotime. The pseudotime was calculated with predicted differentiation trajectories of the following cells: PROG, PC, IPC, Neuron, IN, EX, AS, and OPC. The gray shading indicates confidence intervals computed by the generalized additive model approximation. C Volcano plot of gene expression altered by vascularization in neurons. D GSEA plots of GO terms predicted from the significantly altered (adjusted p-value < 0.01) gene groups. Left panel: GO terms involved in neurodevelopment (nervous system development, neuron development, neuron projection), right panel: GO terms involved in apoptosis (apoptotic signaling pathway). In HUVEC co-culture samples for 100 days, GO terms were not predicted because of the low number of genes altered by vascularization