The gene list for transcriptional and epigenetic regulatory factors were obtained from AnimalTFDB v2.0 (Zhang et al., 2012). After removing regulatory factors not expressed in any cells, we calculated Pearson correlation coefficient with all pairwise comparison. The co-expressed network of regulatory factors was constructed by connecting them with more than 0.125 correlation coefficient. Transcription factors were grouped using edge.betweenness.community function and network graph was drawn by graph.adjacency function in igraph R package (v1.0.1) (Figure 5J). Public RNA-seq data by C1 Fluidigm system from human fetal and adult healthy cortex were downloaded from NCBI Short Read Archive (SRP057196) (Darmanis et al., 2015). As shown above, mapping and calculation of gene expression level were performed by Tophat2 and Cufflinks software, respectively. Gene signatures of NPC and newly born neuron were obtained by 4-fold change and T test p-value <0.05 between replicating and quiescent neuron (Figure S4B). Gene signatures for AS, OLand OPC were obtained by comparing each cell type to the other cells with the same threshold (Figure S4E).
