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

Hanni Willenbrock, Jesper Salomon, Rolf Søkilde, Kim Bundvig Barken, Thomas Nøhr Hansen, Finn Cilius Nielsen, Søren Møller, Thomas Litman

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    Abstract

    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.
    Original languageEnglish
    JournalRNA: A publication of the RNA Society
    Volume15
    Issue number11
    Pages (from-to)2028-34
    Number of pages6
    ISSN1355-8382
    DOIs
    Publication statusPublished - 2009

    Bibliographical note

    Keywords: Gene Expression; MicroRNAs; Oligonucleotide Array Sequence Analysis; Reproducibility of Results; Sequence Analysis, RNA

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