With neuronal differentiation, transcripts associated with pluripotency, positive control of the cell cycle, and many chromatin remodeling factors were downregulated, whereas genes involved in signaling, transcripts associated with anterior-posterior patterning (HOX genes) and SOX genes were induced with differentiation. Cell surface molecules, many involved in neurite outgrowth, and transcripts that encode membrane channels were also upregulated with neuronal differentiation. Transcripts involved in early neuronal differentiation including ELAVL1,2,3,4; FOXP1; MAP2; MAPT; MBD2; NEFL, NEFM and NRG1–4 were increased, whereas genes associated with glial lineage differentiation were not identified in BP, but GFAP was present in controls. Transcripts previously suggested to be dysregulated in BP, including ANK3, CACNA1C, GSK3β (glycogen synthase kinase 3 beta), MECP2, NCAN, SYNE1 and ZNF804A, were significantly upregulated as both control and BP iPSC differentiated to neurons, whereas BDNF and DISC1 were not changed.
