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Whole genome transcriptome polymorphisms in Arabidopsis thaliana

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

Author Affiliations

Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA

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Genome Biology 2008, 9:R165 doi:10.1186/gb-2008-9-11-r165

Published: 24 November 2008

Abstract

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.