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

Additional files

Additional file 1:

Validation of microarray data generated by different platforms. Differential expression of a selection of genes after infection with MHV at 6 h p.i. is shown as determined by two different microarray platforms, with or without vRNA depletion, and by quantitative RT-PCR. Note that the genes from the different groups (i.e. false positive hits, additional hits, and hits by both platforms and both methods), were randomly selected for RT-PCR validation.

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Additional file 2:

QC metrics of Affymetrix Genechips^®. Reported QC metrics are shown for each individual array (Chip ID), including scale factor (SF), noise (RawQ), average background signal (Bg Avg), average noise signal (Noise Avg), number of probe sets detected (#P), percent probe sets detected (%P), mean signal for all probe sets (Signal(All)), and β-actin and GAPDH 5'/3' ratios.

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