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Genome Biology

, 9:R165

First Online: 24 November 2008Received: 30 August 2008Revised: 01 November 2008Accepted: 24 November 2008


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 multi-dimension and high resolution.

AbbreviationsASEallele specific expression

eQTLexpression quantitative trait loci

FDRfalse discovery rate

HMMhidden Markov model

RT-PCRreverse transcription PCR

SFPsingle feature polymorphism.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2008-9-11-r165 contains supplementary material, which is available to authorized users.

Xu Zhang, Jake K Byrnes contributed equally to this work.

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Author: Xu Zhang - Jake K Byrnes - Thomas S Gal - Wen-Hsiung Li - Justin O Borevitz

Source: https://link.springer.com/


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