Predominant cell types in each primary cortical cell population were identified using known marker genes, and visualized by taking the average expression across population replicates, clustering these data using marker genes, and plotting the results as a heat map. Gate P09 populations, which showed highest expression of SST interneuron markers, were then directly compared with in vitro interneuron populations. First, data from both sets of populations were log transformed by taking Log2(FPKM+1), and absent genes (FPKM>1 in >5% of in vitro populations) were excluded from the analysis. Next, standard principal component analysis (PCA) was performed (using the prcomp R function) on the top 1% most differential genes based on maximum pairwise fold change across 6 groups (DCX+ D24, DCX− D24, DCX+ D54, DCX− D54, DCX+ D100, DCX− D100). Finally, we mapped populations from gate P09 into PCA space to estimate age of in vitro cells, and plotted the results. We note that this analysis is robust to choice of threshold for differentially expressed genes.
