Gene expression arrays

All blood samples were drawn from participants in a stable state of asthma. As previously described¹⁸ lymphoblastoid B cell lines (LCLs) derived from childhood asthmatics were cultured in RPMI 1640 medium (Sham-treated LCLs) and treated with Dex (10⁻⁶ M) for 6 hours (Dex-treated LCLs). PBMCs from adult asthmatics were cultured in the same conditions, that is, RPMI 1640 medium for 6 hours (Sham-treated PBMCs) and Dex (10⁻⁶ M) for 6 hours (Dex-treated PBMCs). Gene expression levels were measured using the Illumina HumanRef8 v2 BeadChip (Illumina, San Diego, CA, USA) for childhood asthmatics and the Affymetrix GeneChip Human Gene 2.0 ST (Affymetrix, Santa Clara, CA, US) for adult asthmatics. We removed probes with bad chromosome annotation, and probes in X or Y chromosome. We then did variance stabilizing transformation and quantile normalization respectively to reduce the effects of technical noises and to make the distribution of expression level for each array closer to normal distribution. We guessed that Sham-treated LCLs from childhood asthmatics or Sham-treated PBMCs from adult asthmatics might represent intrinsic genetic traits of participants and in vitro perturbation by Dex might give us an insight to understand responses to corticosteroid. We attempted to search genes or gene modules associated with AEs using both transcriptomic datasets. The expressions of genes of interest were relatively compared using raw intensity values and validated using real-time polymerase chain reaction (PCR).