The iDEGs IRX2 and DPP10 have been linked to neural development or psychiatric disease29-32 and IRX2 suppression reportedly impairs hESC differentiation into neural progenitors. Silencing of IRX2 and DPP10 in some of the hiPSC lines and none of the hESC lines (Fig. 4B) was confirmed by qPCR (Fig. 4C). However, the iDEGs did not affect the cells’ potential to differentiate into neuroectodermal cells using a published protocol33 (Fig. 4D), as determined by RNA expression analysis for NESTIN, SOX1, PAX6, and FOXG1, well- established markers of neuroectoderm differentiation from human pluripotent stem cells34 (Fig. 4E). Consistent with this, PAX6 and SOX1 were equally expressed at the protein level during neural differentiation from hiPSC and hESC GFP lines (Fig. 4F and Supplementary Fig. 3D).
