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Genome Biol. 2008;9(11):R165. doi: 10.1186/gb-2008-9-11-r165. Epub 2008 Nov 24.

Whole genome transcriptome polymorphisms in Arabidopsis thaliana.

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  • 1Department of Ecology and Evolution, University of Chicago, 1101 E, 57th Street, Chicago, IL 60637, USA. xuzhang@uchicago.edu


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.

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