Four BPD patient-derived iPSC clones (ABP03, 05, 07 and 11) and four unaffected sibling-derived (control) iPSC clones (ABP04, 06, 08 and 12), were differentiated into neuronal progenitors (NPs) and neurons as described in Materials and Methods section. S1 Fig shows the key characteristics of the cultures along the stages of neuronal differentiation. L neuronal cultures exhibited characteristic neuronal morphology including axons, dendrites and neurites in addition to positive immunostaining for MAP2 and β-tubulin III (S1 Fig). For microarray studies and further characterization, RNA samples from the four BPD and four controls were collected from NP, E neurons (2 weeks of differentiation) and L neurons (4 weeks of differentiation) as well as undifferentiated iPSCs. Expression of markers of pluripotency and neuronal differentiation were examined using qRT-PCR. The differentiation of iPSCs into NPs resulted in a dramatic decrease in expression of the pluripotency marker, OCT4 (Fig 2A). At the same time, PAX6 and NESTIN expression, early markers of neuroectoderm, increased indicating desired lineage specification (Fig 2B and 2C)[34]. The generation of NPs was further confirmed by increased expression of the dorsoventral neuronal
