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dc.contributor.author Fedrigo, O
dc.contributor.author Warner, LR
dc.contributor.author Pfefferle, AD
dc.contributor.author Babbitt, CC
dc.contributor.author Cruz-Gordillo, P
dc.contributor.author Wray, GA
dc.date.accessioned 2011-06-21T17:32:14Z
dc.date.issued 2010
dc.identifier.citation PLoS ONE, 2010, 5 (9), pp. 1 - 7
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10161/4570
dc.description.abstract Because many species-specific phenotypic differences are assumed to be caused by differential regulation of gene expression, many recent investigations have focused on measuring transcript abundance. Despite the availability of high throughput platforms, quantitative real-time polymerase chain reaction (RT-QPCR) is often the method of choice because of its low cost and wider dynamic range. However, the accuracy of this technique heavily relies on the use of multiple valid control genes for normalization. We created a pipeline for choosing genes potentially useful as RT-QPCR control genes for measuring expression between human and chimpanzee samples across multiple tissues, using published microarrays and a measure of tissue-specificity. We identified 13 genes from the pipeline and from commonly used control genes: ACTB, USP49, ARGHGEF2, GSK3A, TBP, SDHA, EIF2B2, GPDH, YWHAZ, HPTR1, RPL13A, HMBS, and EEF2. We then tested these candidate genes and validated their expression stability across species. We established the rank order of the most preferable set of genes for single and combined tissues. Our results suggest that for at least three tissues (cerebral cortex, liver, and skeletal muscle), EIF2B2, EEF2, HMBS, and SDHA are useful genes for normalizing human and chimpanzee expression using RT-QPCR. Interestingly, other commonly used control genes, including TBP, GAPDH, and, especially ACTB do not perform as well. This pipeline could be easily adapted to other species for which expression data exist, providing taxonomically appropriate control genes for comparisons of gene expression among species. © 2010 Fedrigo et al.
dc.format.extent 1 - 7
dc.language.iso en_US en_US
dc.relation.ispartof PLoS ONE
dc.relation.isversionof 10.1371/journal.pone.0012545
dc.title A pipeline to determine RT-QPCR control genes for evolutionary studies: Application to primate gene expression across multiple tissues
dc.title.alternative en_US
dc.type Journal Article
dc.description.version Version of Record en_US
duke.date.pubdate 2010-9-2 en_US
duke.description.endpage e12545 en_US
duke.description.issue 9 en_US
duke.description.startpage e12545 en_US
duke.description.volume 5 en_US
dc.relation.journal Plos One en_US
pubs.issue 9
pubs.organisational-group /Duke
pubs.organisational-group /Duke/Trinity College of Arts & Sciences
pubs.organisational-group /Duke/Trinity College of Arts & Sciences/Biology
pubs.organisational-group /Duke/Trinity College of Arts & Sciences/Evolutionary Anthropology
pubs.volume 5

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