Weighted gene co-expression network analysis (WGCNA) was performed to identify modules of co-expressed genes, and the genes were then used to cluster cell types, as described in previously (Figure 4A) (Tasic et al., 2016; Thomsen et al., 2016). We observed 41 cell clusters—8 at D24, 11 at D54, 13 at D100 and 10 at D125—which showed clear separation between progenitor (Cit−) and neuron (Cit+) cells at each time point. Cit− clusters had higher VIM and SOX2 expression, whereas Cit+ clusters expressed more DCX and GAD1 (Padj < 0.001, FDR for Cit+ vs. Cit−).
