expression data set encompassing cerebral cortical development from human embryonic stem cells [51], which classified their RNA-seq samples to five developmental stages: “Pluripotency” (PP: Day 0), “Neural Differentiation” (ND: Day 7), “Cortical Specification” (CS: Day 12), “Deep Layer neuron generation” (DL: Day 26), and “Upper Layer neuron generation” (UL: Day 63). Principal component analysis (PCA) indicates that our samples were mapped to a stage between Day 12 (the start of the CS stage) and Day 19 (Additional file 4: Figure S2B, PC1), suggesting that our samples likely had passed the peak of neuron differentiation and were undergoing specification of neuronal subtypes. Again, in this analysis our control and SZ samples were grouped together and mapped to the same differential stages. Finally, we looked into a number of markers for glutamatergic and GABAergic neurons, and astrocytes, which were expressed at least in one of our samples (Additional file 4: Figure S2C), and found that glutamatergic and GABAergic markers had relatively high expression levels, while markers for astrocytes and other subtypes were either not expressed or expressed at relatively low levels.
