Genome-Scale Validation of Deep-Sequencing Libraries 英文参考文献.docVIP

Genome-ScaleValidationofDeep-SequencingLibraries DominicSchmidt1,2.,RoryStark1.,MichaelD.Wilson1,GordonD.Brown1,DuncanT.Odom1,2* 1Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, 2Department of Oncology, Hutchison/MRC Research Centre, Cambridge,UnitedKingdom Abstract Chromatinimmunoprecipitationfollowedbyhigh-throughput(HTP)sequencing(ChIP-seq)isapowerfultooltoestablish protein-DNAinteractionsgenome-wide.Theprimarylimitationofitsbroadapplicationatpresentistheoften-limitedaccess to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximizetheefficiencyoflibrarycreationandquicklygeneratereliablepreliminarydataonachromosomalscaleinadvance ofdeepsequencing.Wealsoexploitthistechniquetocompareenrichedregionsidentifiedusingmicroarrayswiththose identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizingtheadditionalenrichedregionsidentifiableusingHTPsequencing. Citation: Schmidt D, Stark R, Wilson MD, Brown GD, Odom DT (2008) Genome-Scale Validation of Deep-Sequencing Libraries. PLoS ONE 3(11): e3713. doi:10.1371/journal.pone.0003713 Editor:Ju¨rgBa¨hler, WellcomeTrustSangerInstitute,UnitedKingdom ReceivedSeptember29,2008;AcceptedOctober21,2008;PublishedNovember12,2008 Copyright: ? 2008 Schmidt 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:SupportedbytheEuropeanResearchCouncil(DTO),HutchinsonWhampoa(DTO),UniversityofCambridge(DTO,DS),andtheCancerResearchUK (DTO,DS,RS,MDW).Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:The