Supplementary Figure 1: Characterization of iPSC-derived neural stem cells (NSCs).

a, Quantitative real time PCR assay for assessing retroviral transgene silencing for c-MYC, OCT3/4, KLF4 and SOX2 in ASD and control iPSC lines. Values represent means ± s.e.m. from n = 3 independent cell culture replicates. b, Schema showing directed differentiation of subject-derived iPSCs into functional neurons. c, Representative confocal images of iPSC-derived NSCs that show homogeneous expression of the markers Nestin and Pax6. Scale bar 50 μm. Experiments were performed in all 13 subject lines and 4 cell culture replicates each with similar results. d, Immunofluorescence images of six-week-old neurons stained with βIII-tubulin (Tuj1), Map2ab and vGlut1. Scale bar 100 μm (left) and 10 μm (right). The staining was repeated in all 13 subject lines at least once with similar results. e, Stereological counts of iPSC-derived NSCs expressing Nestin and PAX6. Values represent means ± s.e.m. from n = 3 independent cell culture replicates. f, Quantitative real time PCR assay for assessing the expression of the anterior marker PAX6. Values represent means ± s.e.m. from n = 3 independent cell culture replicates. g, Representative confocal images of iPSC-derived NSCs that show expression of Nestin and the forebrain-associated marker FoxG1. Scale bar 50 μm. Immunohistochemistry was performed in all 13 subject lines with 4 cell culture replicates each. h, Quantification of FoxG1-positive iPSC-derived NSCs across all subject cell lines. Box plots show median (center line) and interquartile range (IQR), with whiskers representing the minimum and maximum; n = 4 independent cell culture replicates.