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Microarrays, deep sequencing and the true measure of the transcriptome

John H Malone* and Brian Oliver

Author affiliations

Laboratory of Cellular and Developmental Biology, National Institute of Digestive, Diabetes, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA

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Citation and License

BMC Biology 2011, 9:34  doi:10.1186/1741-7007-9-34

Published: 31 May 2011


Microarrays first made the analysis of the transcriptome possible, and have produced much important information. Today, however, researchers are increasingly turning to direct high-throughput sequencing - RNA-Seq - which has considerable advantages for examining transcriptome fine structure - for example in the detection of allele-specific expression and splice junctions. In this article, we discuss the relative merits of the two techniques, the inherent biases in each, and whether all of the vast body of array work needs to be revisited using the newer technology. We conclude that microarrays remain useful and accurate tools for measuring expression levels, and RNA-Seq complements and extends microarray measurements.