Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

• Published in: RNA (Cambridge) Vol. 15; no. 11; pp. 2028 - 2034
• Main Authors: Willenbrock, Hanni, Salomon, Jesper, Søkilde, Rolf, Barken, Kim Bundvig, Hansen, Thomas Nøhr, Nielsen, Finn Cilius, Møller, Søren, Litman, Thomas
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.11.2009
• Subjects: Gene Expression; MicroRNAs - analysis; MicroRNAs - chemical synthesis; MicroRNAs - genetics; Oligonucleotide Array Sequence Analysis - methods; Reproducibility of Results; Sequence Analysis, RNA - methods
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.1699809

Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.