Post-mortem PFC grey matter tissue homogenates were obtained from all subjects. Total RNA was extracted, amplified and fluorescently labelled. Reference RNA was pooled from all samples and treated identically to sample RNAs. Labelled RNAs were hybridized to two-colour custom-spotted arrays from the NHGRI microarray core facility. After normalization21, log2 intensity ratios were further adjusted to reduce the impact of known and unknown sources of systematic noise on gene expression measures using surrogate variable analysis22 (SVA). Validation of microarray expression patterns was performed by Taqman qPCR (Supplementary Table 8). In this study of RNA derived from tissue homogenates, differential gene expression within a population of cells stable in cell type is indistinguishable from a change in the abundance of cell types that express different genes. There is no doubt that both phenomena contribute to signals measured here in the prefrontal cortex.
