Single-Species Microarrays and Comparative Transcriptomics 英文参考文献.docVIP

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Single-Species Microarrays and Comparative Transcriptomics 英文参考文献.doc

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Single-Species Microarrays and Comparative Transcriptomics 英文参考文献

Single-SpeciesMicroarraysandComparative Transcriptomics Fre′de′ricJ.J.Chain1,DoraIlieva2,BenJ.Evans1* 1Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario, Canada, 2Michael DeGroote School of Medicine, McMaster University,Hamilton,Ontario,Canada Abstract Background: Prefabricated expressionmicroarraysarecurrentlyavailableforonlyafewspecies butmethodshavebeen proposedtoextendtheirapplicationtocomparisonsbetweendivergentgenomes. Methodology/PrincipalFindings:HerewedemonstratethatthehybridizationintensityofgenomicDNAisapoorbasison whichtoselectunbiasedprobesonAffymetrixexpressionarraysforstudiesofcomparativetranscriptomics,andthatdoingso producesspuriousresults.WeusedtheAffymetrixXenopuslaevismicroarraytoevaluateexpressiondivergencebetweenX.laevis, X.borealis,andtheirF1hybrids.Whendataareanalyzedwithprobesthatinterrogateonlysequenceswithconfirmedidentityin bothspecies,werecoverresultsthatdiffersubstantiallyanalysesthatusegenomicDNAhybridizationstoselectprobes. Conclusions/Significance: Ourfindings haveimplications for theexperimental designof comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploidspecies. Citation: Chain FJJ, Ilieva D, Evans BJ (2008) Single-Species Microarrays and Comparative Transcriptomics. PLoS ONE 3(9): e3279. doi:10.1371/ journal.pone.0003279 Editor:DawnN.Albertson,MinnesotaStateUniversityMankato,UnitedStatesofAmerica ReceivedAugust4,2008;AcceptedSeptember4,2008;PublishedSeptember25,2008 Copyright: ? 2008 Chain et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding: This research was supported b