Human cell types engineered from induced pluripotent stem cells (iPSCs) through transcription factor overexpression are widely used to study the mechanisms controlling cell fate differentiation, to model human diseases, and to identify potential therapies (Guo and Morris, 2017). Human neurons can be generated through the forced expression of the transcription factor neurogenin 2 (NGN2) with high efficiency and reproducibility (Zhang et al., 2013). These NGN2-induced neurons (NGN2-iNs) functionally mature into morphologically complex and electrophysiological active neurons after approximately 3–4 weeks of co-culture with astrocytes. The NGN2-iN system has been used extensively to understand neuron development and model disease (Lin et al., 2018). However, the characterization of NGN2-iNs so far has generally been limited to functional assays, biomarker expression, and bulk transcriptomics. There is a lack of comprehensive transcriptomic comparison with primary neuron subtypes and it is unclear whether any off-target fate emerges during the differentiation process. Single-cell sequencing methods provide powerful resolution into the heterogeneity of directed differentiation culture systems (Biddy et al., 2018, 2018, 2018; Camp et al., 2018; Karow et al., 2018). Previously, we have used single-cell mRNA
