Improved microarray gene expression profiling of virus-infected cells after removal of viral RNAReport as inadecuate

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 9:221

First Online: 14 May 2008Received: 29 January 2008Accepted: 14 May 2008


BackgroundSensitivity and accuracy are key points when using microarrays to detect alterations in gene expression under different conditions. Critical to the acquisition of reliable results is the preparation of the RNA. In the field of virology, when analyzing the host cell-s reaction to infection, the often high representation of viral RNA vRNA within total RNA preparations from infected cells is likely to interfere with microarray analysis. Yet, this effect has not been investigated despite the many reports that describe gene expression profiling of virus-infected cells using microarrays.

ResultsIn this study we used coronaviruses as a model to show that vRNA indeed interferes with microarray analysis, decreasing both sensitivity and accuracy. We also demonstrate that the removal of vRNA from total RNA samples, by means of virus-specific oligonucleotide capturing, significantly reduced the number of false-positive hits and increased the sensitivity of the method as tested on different array platforms.

ConclusionWe therefore recommend the specific removal of vRNA, or of any other abundant -contaminating- RNAs, from total RNA samples to improve the quality and reliability of microarray analyses.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-9-221 contains supplementary material, which is available to authorized users.

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Author: Matthijs Raaben - Penn Whitley - Diane Bouwmeester - Robert A Setterquist - Peter JM Rottier - Cornelis AM de Haan


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