title: Using DNA microarray to study human cytomegalovirus gene expression.
abstract: DNA microarray technology has become one of the most widely used tools for functional genomics and is playing an ever increasing role in the study of viral infections and host-pathogen interactions. This paper describes the development of an oligonucleotide microarray representing all the predicted open reading frames of the human cytomegalovirus (HCMV) and an established protocol for simultaneously measuring the expression of all HCMV genes. To evaluate the performance of the HCMV array, human foreskin fibroblasts were either mock infected or infected with the HCMV AD169 or Toledo strains. Hybridizations were performed to determine the level of detection of HCMV transcripts from both the AD169 and Toledo strains and to assess reproducibility within and between slides. Overall, approximately 95% of the predicted HCMV genes produced detectable levels of mRNA, with median signal to noise and signal to background ratios of 41 and 14, respectively. Scatter plots of samples within an array and between two arrays resulted in average linear regressions above 0.95 and 0.9, respectively, indicating that data from the arrays are highly reproducible. In addition, transcripts from genes found in the Toledo strain but not in AD169 were specifically detected.
authors.affiliation: Department of Microbiology and Molecular Genetics, New Jersey Medical School, UMDNJ, International Center for Public Health, 225 Warren Street, Newark, NJ 07103-1709, USA.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Yang
authors.forename: Saleena
authors.initials: S
authors.lastname: Ghanny
authors.forename: Weijia
authors.initials: W
authors.lastname: Wang
authors.forename: Anthony
authors.initials: A
authors.lastname: Galante
authors.forename: Walter
authors.initials: W
authors.lastname: Dunn
authors.forename: Fenyong
authors.initials: F
authors.lastname: Liu
authors.forename: Patricia
authors.initials: P
authors.lastname: Soteropoulos
authors.forename: Hua
authors.initials: H
authors.lastname: Zhu
mesh_terms: D002460:Cell Line; D003587:Cytomegalovirus / Q000235:genetics*; D005347:Fibroblasts / Q000821:virology; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis; D012367:RNA, Viral / Q000032:analysis; D015203:Reproducibility of Results
chemical_list: D012333:RNA, Messenger; D012367:RNA, Viral