In order to validate the differential expression of genes in the BD patient-derived cells that was observed in the PsychGene NanoString profiles, and in order to specifically characterize the BD patient-derived cells in greater depth, we performed genome-wide, transcriptome analysis using RNA-sequencing (RNA-seq) to compare the BD patient CXCR4+ NPCs and parental control CXCR4+ NPCs since this was the cell state that showed the earliest evidence of multiple robust phenotypic differences in the NanoString analysis. Total RNA was collected from each of the parental CXCR4+ NPC lines and replicate cultures of one of the BD patient CXCR4+ NPCs. Tophat was used to align raw RNA-seq reads to the Ensembl human transcriptome followed by Cuffdiff v1.0 identification of differentially expressed genes from averaged reads from both parents and averaged reads from both replicates of the BD CXCR4+ NPCs. In total, 15,803 transcripts, including both coding and non-coding transcripts were measured with sufficient coverage in both samples, of which 503 were found to have nominally significant differential expression (p<0.05), which after correction for multiple hypothesis a total of 35 were considered significantly expressed (p<0.05, Benjamini-Hochberg) (Sup. Table 10).
