Validation of microarrays using qRT-PCR.

<p>Mean±S.E.M of fold change in gene expression in T2D patients, as compared to controls, is shown for (A) female visceral adipose, (B) male visceral adipose, (C) male skeletal muscle, and (D) female subcutaneous adipose. Fold change was calculated for two to six technical replicates, each representing three biological replicates. The source of RNA used in qRT-PCR analysis was same as in microarray profiling. A total of 47 genes were used for validation. The rationale behind the subsets of genes selected was two fold. One, the genes should represent, wherever applicable, one or more enriched pathways (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053522#pone-0053522-t003" target="_blank"><b>Table 3</b></a>) in a given condition. Second, the genes should maximally represent those which are differentially expressed at adjusted <i>p</i> value cutoff (<b>Dataset S4</b>) in more than one condition, so that validation of microarrays can be examined more widely. The selected genes, besides others, covered all the pathways that were enriched in the above microarray gene lists. Notably, up- or down- regulation observed in qRT-PCR, shown in red and green, respectively, was consistent with microarrays, for all comparisons.