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Better together: multiplexing samples to improve the preparation and reliability of gene expression studies

Nature Methods volume 12, pages 304–305 (2015)Cite this article

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Two methods for early tagging of sample RNA before RT-qPCR or full RNA-seq open the door to experiments with fewer technical batch effects.

Gene expression studies can be divided into two groups according to the number of samples involved. Studies with a few samples and few replicates are done typically with RNA-seq, which offers the ability to quantify known genes and potentially discover new genes and transcripts. The primary reason that RNA-seq studies are not done on larger sample numbers is not the cost of sequencing itself—the sequencing of samples to a moderate depth of 10–20 million reads is affordable—but the cost and efforts involved in preparing the samples for sequencing. A majority of the larger studies involving more than a few dozen samples instead still use microarrays or reverse-transcription quantitative PCR (RT-qPCR) with a panel of gene candidates. Two papers in this issue improve sample preparation using molecular tagging of RNA1,2.

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Figure 1: Early parallelization of samples to increase throughput and uniformity.

Katie Vicari/Nature Publishing Group

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Authors and Affiliations

  1. Ali Mortazavi is in the Department of Developmental and Cell Biology, and at the Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA.,

    Ali Mortazavi

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  1. Ali Mortazavi
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Correspondence to Ali Mortazavi.

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The author declares no competing financial interests.

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Mortazavi, A. Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. Nat Methods 12, 304–305 (2015). https://doi.org/10.1038/nmeth.3333

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