Supplementary Figure 6: RNA-seq analysis of 4 healthy control and 4 schizophrenia cINs from three independent differentiations.

Related to Fig. 3. The lines used in this experiment are summarized in Supplementary Table 3. (a) Number of reads generated. Rate (%) = Read number of Pseudoaligned / Read number of Input x 100. (b) Total detected gene number. The gene numbers were counted for those with RPKM > 1. (c) Average of pairwise comparison r² values. iPSC RNA-seq r² values are from this study (n = 12 differentiations), while postmortem RNA-seq r² values were calculated from a publicly available RNA-seq dataset (accession number of GSE87194, n = 19 subjects). (d) Principal component analysis of healthy control and schizophrenia cINs (n = 12 differentiations). (e) Principal component analysis of iPSCs (n = 3 lines), healthy control or schizophrenia cINs (n =12 differentiations), and fibroblasts (n = 3 lines). RNA-seq data of iPSC and fibroblasts were from Choi et al. (Choi, J., et al. A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs. Nature biotechnology 33, 1173-1181 (2015)). (f) Table of differentially expressed (DE) genes between 4 healthy control and 4 schizophrenia cINs in three independent differentiations (n=12 differentiations) with adjusted p<0.1. Differential expression was analyzed in R by the Voom function in Limma with adjusted multiple testing.