moderated t-statistics from the Bioconductor package limma [33] to compare treated and control mice. MicroRNAs were considered DE at a nominal value ≤ 0.05. A nominal, rather than FDR-corrected, p value was utilized to preserve as much DE information as possible for our subsequent systems-level analyses as use of an overly-stringent statistical cutoff would cause us to lose valuable network relationships. Although depleted RNA samples precluded confirmation of our results by RT-qPCR, we have used RT-qPCR to validate this microRNA array platform in a previous publication [7]. In that study, RT-qPCR confirmed microRNA expression changes for six different microRNA families in both mouse and human brain tissue.
