Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse fibroblasts infected with murine hepatitis virus using two array platforms to compare the potential for interference from viral RNA

ABSTRACT: Infection of cells with murine hepatitis virus strain A59 (MHV-A59) results in massive amounts of viral RNA within infected cells. When applying transcriptional profiling by means of microarray analysis, this could potentially cause problems since high amounts of viral RNA could in theory interfere with the analysis. Since coronavirus RNAs are polyadenylated, the viral RNAs are also amplified by oligo(dT) primers (a standard procedure when processing RNA samples for array hybridization). In this experiment we compared two different array platforms for the potential interference of viral RNA, using MHV-A59 infection of LR7 (murine fibroblasts) as a model.

INSTRUMENT(S): G2565AA DNA microarray scanner [Agilent]

ORGANISM(S): Mus musculus

SUBMITTER: Matthijs Raaben 

PROVIDER: E-MEXP-1373 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Raaben Matthijs M   Whitley Penn P   Bouwmeester Diane D   Setterquist Robert A RA   Rottier Peter J M PJ   de Haan Cornelis A M CA  

BMC genomics 20080514

<h4>Background</h4>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 investigate  ...[more]

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