Comparison of microarray and quantitative real-time PCR methods for measuring MicroRNA levels in MSC cultures

The capacity for self-renewal and the multilineage potential of mesenchymal stromal cells (MSC) offer a therapeutic promise for regenerative medicine. MicroRNAs (miRNAs) are small noncoding RNAs that play a key regulatory role during differentiation both at the level of posttranslational modulation and epigenetic control. Studies on MSCs have just begun to identify miRNA profiles in MSC and differentiated MSC. While several methods are available for miRNA exploration, microarrays and quantitative real-time PCR (qPCR) are the most common. Since there are several microarray and qPCR platforms available for miRNA detection, it is valuable to explore how these methods compare. We used the NCode Multi-Species miRNA microarray (Invitrogen) and the TaqMan Human microRNA array (Applied Biosystems) to compare microRNA expression in undifferentiated MSCs and MSCs differentiated into early osteoblasts. We show that while there is a somewhat low correlation between these two methods, there is a subset of miRNA measurements that did correlate.