Profiling Gene Expression from Blood Samples

Blood samples were stored at 4 °C on the day of collection until they were shipped overnight each day to our blood processing laboratory in Boston, MA in an insulated container with a cooler pack to keep samples chilled. Upon arrival, RNA was extracted using the Qiagen RNAEasy extraction kit, according to protocol and then stored at −80 °C until analysis. Gene expression profiling was conducted using the Illumina HumanHT-12 v4 Expression BeadChip, with RNA labeling and array hybridization performed according to protocol. Image capture was performed using the Illumina BeadArray Reader. Standard QC and preprocessing procedures were applied to remove failed samples (n = 2). Standard background correction and normalization procedures (Variance-Stabilizing Transform, [16 (link)]) were applied using the R package lumi. The final data set included information from 47,295 probes on 165 samples from 63 subjects.