Expression profiling was performed largely as previously described (Gibbs et al., 2010). RNA was biotinylated and amplified using the Illumina® TotalPrep-96 RNA Amplification Kit and directly hybridized onto HumanHT-12_v3 Expression BeadChips. Where possible, the same RNA samples were used from our previous study that used HumanRef8 Expression BeadChips. Raw intensity values for each probe were normalized using cubic spline in BeadStudio (Illumina) then log2 transformed. Individual probes were included in analysis if they were detected (P < 0.01) in more than 95% of samples in the series.
