We performed scRNA-seq on hESC-derived MGE-like cells at D24, D54, D100 and D125 to characterize transcriptomic changes with single cell resolution. Progenitors (Cit−) or neurons (Cit+), were dissociated, sorted and prepared for scRNA-seq (Picelli et al., 2014)(Figure S4). To determine the maturation landscape and relationship between cells, we performed PCA based the top 1% of differentially expressed genes across all populations based on maximum pairwise fold change (Figure 3A). PCA plots using 10% or 100% of expressed genes were also generated, and result in separation of progenitors and neurons as well as cells in various states of maturation (Figure S5). The first two PCs correspond to Cit expression status and days in culture, allowing us to define the temporal order of these cells by differentiation stage (PC 1) and pseudotime (relative maturity based on gene expression; PC 2), respectively. Progenitors and neurons largely grouped in gene expression space by Cit status; however, some Cit− cells mapped with neurons and vice versa, and a small number of cells (~8.3%) mapped to an intermediate differentiation stage. Similarly, neurons and progenitors both grouped
