hGPCs assessed for gene expression were first sorted by fluorescence-activated cell sorting on the basis of the cell surface marker CD140a (BD Pharmingen) as described (Sim et al., 2011) (Figure S2). Using polyA-selection, mRNA was isolated from these PDGFRα+ hGPCs, which were derived from iPSCs made from 4 patients with juvenile-onset schizophrenia (SCZ line numbers 8 [n=4 independent cell preparations], 29 [n=3], 51 [n=7], and 164 [n=8]); and 3 demographically similar healthy controls (CTR lines 22 [n=3], 37 [n=4], and 205 [n=7]). Sequencing libraries were prepared using the TruSeq RNA v2 kit, and sequenced on an Illumina HiSeq 2500 platform for approximately 45 million 1×100 bp reads per sample. The sequencing reads were pre-processed by trimming off adapter and low-quality sequences from the 3’ end using Trimmomatic (Bolger et al., 2014). The quality of reads before and after pre-processing was assessed with FastQC (D’Antonio et al., 2015), and the pre-processed reads were then aligned to the RefSeq NCBI reference human genome version GRCh38 (Pruitt et al., 2007) with Subread read aligner (Liao et al., 2013) using Hamming distance to break
