Profiling the miRNome: Detecting Global miRNA Expression Levels with DNA Microarrays

The ability to profile the miRNome (global microRNA/miRNA expression levels) accurately has become essential for multiple aspects of biological research. However, this process is complicated by the short length of the mature miRNA, the existence of multiple intermediate miRNA forms, and highly similar mature miRNA sequences amongst miRNA family members. Here, we review the process of experimental design and sample preparation for a miRNome profiling experiment. The essential need for careful sample quality control is also discussed. Several solutions have emerged using DNA microarray hybridization-based platforms that have been developed specifically for miRNA expression analysis. Commercially available miRNA expression profiling platforms from Affymetrix, Agilent, Exiqon, and Invitrogen are compared and contrasted. Finally, we detail the steps for data preprocessing, normalization, and statistical analysis to identify differentially expressed miRNAs. This review will help guide potential users of this relatively new technology in making informed choices during the miRNome profiling process, from initial experimental design to final data analysis.