To characterize the neuronal fate and maturity of our differential neurons, we compared gene expression profiles of our samples with two independent datasets. The first one is based on single cell RNA-seq analysis of human adult cortical samples in which all major cell types (astrocytes, endothelial, microglia, neurons, oligodendrocytes and oligodendrocyte progenitors) of the adult brain were identified [49]. Using the top 5,000 most variable genes in this dataset (which were enriched for signature genes in different cell types) [50], we performed non-metric multidimensional scaling after normalizing expression data across samples and batch correction. The plot of the transformed data in the first two dimensions (Additional file 4: Figure S2A) indicates that our neuronal samples were most similar to populations of adult neurons, with no separation of the 22q11.2 deletion samples from controls. The second one is a temporal gene 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”
