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Series GSE13437 Query DataSets for GSE13437
Status Public on Dec 01, 2008
Title p53 regulates viral gene expression during infection with human cytomegalovirus
Platform organisms Homo sapiens; Human betaherpesvirus 5
Sample organisms Homo sapiens; Human herpesvirus 5 strain Towne
Experiment type Expression profiling by array
Summary Human cytomegalovirus (HCMV) is a common cause of morbidity and mortality in immunocompromised and immunosuppressed individuals. During infection, HCMV is known to employ host transcription factors to facilitate viral gene expression. To further understand the previously observed delayed viral replication and protein expression in p53 knockout cells, we conducted microarray analyses on p53+/+ and p53-/- immortalized fibroblast cell lines. At 12 hpi, applying the significance criteria defined above, no genes showed a significant difference in any of the comparisons. At 24 hpi, we found 19 genes to be significantly different in the THF versus p53-/- comparison and 14 genes to be significantly different in the HFF versus p53-/- comparison. Eleven genes were shared between HFF and THF cells when compared to p53-/- cells (UL30, UL54, UL63, UL65, UL69, UL75, UL110, UL122, IRL4, IRS1, TRS1, shown in bold in Table 1). Eight genes were unique in the THF versus p53-/- comparison (UL48, UL68, UL84, UL100, UL106, UL109, UL111, RL5A), and three genes in the HFF versus p53-/- cell comparison (UL14, UL16, US2). When comparing HFF and THF cells, only US2 showed a significant difference. The ratio (HFF versus p53-/- divided by THF versus p53-/-) of the expression levels of the eleven shared genes from the HFF versus p53-/- and THF versus p53-/- comparisons was an averaged 1.2, indicating that, with the exception of US2, these two cell lines behaved similarly with respect to p53-driven viral gene expression.

Keywords: time course, virus, cytomegalo, hhv5, infection, p53
Overall design Each slide consisted of 4 arrays. Each array consisted of 305 control features, 1265 cellular gene features and 670 viral gene features. The study was performed on 6 slides (HFF-THF, HFF-p53-/-, THF-p53-/- at 12 and 24 hpi). 3 arrays per slide were hybridized with 3 biological replicates of labelled RNA, the 4th array was hybridized with an equimolar mixture of the 3 biological replicate samples. This array was used for control purposes only, and the results were not used for downstream calculations. Each slide was stripped and reprobed two times to provide 3 technical replicates of each sample. As our experiments concentrated on viral genes and their expression, cellular genes were not further analyzed in this study.
Contributor(s) Hannemann H, Rosenke K, O'Dowd J, Fortunato EA
Citation(s) 19224996
Submission date Nov 03, 2008
Last update date Mar 20, 2012
Contact name Holger Hannemann
Phone 2088859237
Organization name University of Idaho
Department MMBB
Lab Lee Fortunato
Street address PO Box 443052
City Moscow
State/province ID
ZIP/Postal code 83843
Country USA
Platforms (1)
GPL7474 University of Idaho_Fortunato_homo-HHV5_2240
Samples (18)
GSM339216 HFF 12hpi Rep 1
GSM339217 HFF 12hpi Rep 2
GSM339218 HFF 12hpi Rep 3
BioProject PRJNA110027

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE13437_Comparison_values.txt 236.1 Kb (ftp)(http) TXT
GSE13437_RAW.tar 570.0 Kb (http)(custom) TAR (of TXT) 182.4 Kb (ftp)(http) ZIP
Processed data included within Sample table

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