Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA

Matthijs Raaben¹ , Penn Whitley² , Diane Bouwmeester³ , Robert A Setterquist² , Peter JM Rottier¹ and Cornelis AM de Haan¹

¹Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands

²Ambion Inc, Research & Development, 2170 Woodward St, 78744 Austin, TX, USA

³University Medical Center Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands

author email corresponding author email

BMC Genomics 2008, 9:221doi:10.1186/1471-2164-9-221


Published:	14 May 2008

Abstract

Background

Sensitivity 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.

Results

In 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.

Conclusion

We 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.