To characterize the iPSC and to determine whether there were differences in their gene expression profiles with neuronal differentiation, total RNA was isolated from six individual iPSC cell lines (3 BP patients and 3 controls (C)) before and following 8 weeks of neuronal differentiation using the TRIzol reagent (Invitrogen, 15596-026). RNAs were DNased followed by the RNeasy MinElute Cleanup reagent (Qiagen, Hilden, Germany, 74204). RNA quantity and quantity were measured in an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) producing RNAs with an integrity measure > 9.5. They were amplified and hybridized to GeneChip U133 Plus 2.0 microarrays (Affymetrix, Santa Clara, CA, USA). Data quality control parameters included scaling factor, noise, background, percentage of present calls, 5′/3′ signal ratios observed in GAPDH mRNA and 5′/3′ signal ratios of spiking genes. Raw data (U133P2 CEL files) were processed using the Bioconductor package ‘Affy' for R. Normalized Log2 transformed probe intensity Robust Multi-chip Average values were used in differential gene expression analyses and transcripts with significantly altered expression (P⩽0.05) between BP and controls were identified using t-test with R and
