Fig 2: COS hiPSC cohort reprogramming and differentiation. a Validated hiPSCs (from 14 individuals with childhood-onset-schizophrenia (COS) and 12 unrelated healthy controls) and NPCs (12 COS; 12 control individuals) yielded 94 RNA-Seq samples (11 COS; 11 control individuals). b Schematic illustration of the reprogramming and differentiation process, noting the yield at each stage. c Sex breakdown of the COS-control cohort. d Breakdown of SZ-associated copy number variants in the 11 COS patients with RNA-Seq data. e Representative qPCR validation of NANOG, NESTIN, and SYN1 expression in hiPSCs (white bar), NPCs (light gray) and 6-week-old neurons (dark gray) from three individuals. f FACS analysis for pluripotency markers TRA-1-60 (left) and SSEA4 (right) in representative control (blue, n = 17) and COS (red, n = 16) hiPSCs. g FACS analysis for NPC markers SOX2 (left) and NESTIN (right) in control (blue, n = 34) and COS (red, n = 37) NPCs. h Representative images of NPCs (left) and 6-week-old forebrain neurons (right) from control (top) and COS (bottom). NPCs stained with SOX2 (red) and NESTIN (green); neurons stained with MAP2 (red). DAPI-stained nuclei (blue). Scale bar=50 μm. i Computational workflow showing quality control, integration with external data sets, computational deconvolution with Cibersort, decomposition multiple sources of expression variation with variancePartition, coexpression analysis with WGCNA, differential expression and concordance analysis

Fig 3: Ratio of marker expression in donor ESCs relative to embryonic cells. Intensity levels for expression of (A) Nanog, (B) Oct4 and (C) Sox2 in ESCs relative to average expression level for host embryo cells. Values at the top (A) indicate number of chimaeras inspected at different time points. Each black dot represents expressions levels for a single ESC relative to the host. Each box plot is overlaid with data distributed along x-axis for clarity; red lines indicate mean values, grey box is s.e. Intensity of fluorescence was detected using Volocity (see the Materials and Methods).

Fig 4: Gene expression and protein levels of pluripotent and cardiomyocyte markers in hiPSC-CMs. Gene expression was determined by qPCR using primers specific for OCT4 (A), SOX2 (B) and TNNT2 (C). OCT4 and SOX2 are markers of pluripotency, and TNNT2 is a late cardiac marker; all values were normalized to β2-microglobulin (β2M) and compared to control day 0. Protein levels were determined by flow cytometry: (D) percent cells positive for both Oct3/4 and Sox2 and (E) percent cells positive for cardiac TnT. Flow cytometry is shown as percent positive cells after gating for live, single cells. Data is shown as mean ± SEM and statistical analysis was done by two-way ANOVA followed by Tukey’s test (n = 3 biological replicates for gene expression, n = 2 biological replicates for flow cytometry; *P < 0.05, **P < 0.01, #P < 0.001 vs. control).