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Whole genome transcriptome polymorphisms in Arabidopsis thaliana

Zhang, Xu; Byrnes, Jake K; Gal, Thomas S; Li, Wen-Hsiung; Borevitz, Justin O

Description

Whole genome tiling arrays are a key tool for profiling global genetic and expression variation. In this study we present our methods for detecting transcript level variation, splicing variation and allele specific expression in Arabidopsis thaliana. We also developed a generalized hidden Markov model for profiling transcribed fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at...[Show more]

dc.contributor.authorZhang, Xu
dc.contributor.authorByrnes, Jake K
dc.contributor.authorGal, Thomas S
dc.contributor.authorLi, Wen-Hsiung
dc.contributor.authorBorevitz, Justin O
dc.date.accessioned2015-12-14T00:25:59Z
dc.date.available2015-12-14T00:25:59Z
dc.identifier.issn1465-6906
dc.identifier.urihttp://hdl.handle.net/1885/94997
dc.description.abstractWhole genome tiling arrays are a key tool for profiling global genetic and expression variation. In this study we present our methods for detecting transcript level variation, splicing variation and allele specific expression in Arabidopsis thaliana. We also developed a generalized hidden Markov model for profiling transcribed fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution.
dc.description.sponsorshipWe thank Andrew Cal for reading the manuscript. XZ was supported by start-up funds to JOB and a NIH grant (R01GM073822) to JOB. JKB was supported by the Department of Education's Graduate Assistance in Areas of National Needs (P-P200A030043) and NIH grants (GM30998 and GM081724) to W-HL. W-HL was supported by NIH grants (GM30998 and GM081724). JOB was supported by a NIH grant (R01GM073822).
dc.format17 pages
dc.publisherBioMed Central
dc.rights© 2008 Zhang et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.sourceGenome Biology
dc.subjectalternative splicing
dc.subjectarabidopsis
dc.subjectgene expression regulation, plant
dc.subjectmarkov chains
dc.subjectgene expression profiling
dc.subjectgenome, plant
dc.subjectpolymorphism, genetic
dc.titleWhole genome transcriptome polymorphisms in Arabidopsis thaliana
dc.typeJournal article
local.description.notesImported from ARIES.
local.identifier.citationvolume9
dcterms.dateAccepted2008-11-24
dc.date.issued2008-11-24
local.identifier.absfor060411
local.identifier.ariespublicationf5625xPUB10737
local.publisher.urlhttp://www.biomedcentral.com/
local.type.statusPublished Version
local.contributor.affiliationZhang, Xu, University of Chicago, United States of America
local.contributor.affiliationByrnes, Jake k , University of Chicago, United States of America
local.contributor.affiliationGal, Thomas S , University of Chicago, United States of America
local.contributor.affiliationLi, Wenhsiung, University of Chicago, United States of America
local.contributor.affiliationBorevitz, Justin, College of Medicine, Biology and Environment, CMBE Research School of Biology, Division of Plant Sciences, The Australian National University
local.identifier.essn1474-760X
local.bibliographicCitation.issue11
local.bibliographicCitation.startpageR165
local.bibliographicCitation.lastpage17
local.identifier.doi10.1186/gb-2008-9-11-r165
local.identifier.absseo970106
dc.date.updated2016-02-24T08:37:05Z
local.identifier.scopusID2-s2.0-57849136008
local.identifier.thomsonID000261273100013
CollectionsANU Research Publications

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