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Open Access Highly Accessed Research article

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

Joshua S Bloom1, Zia Khan2, Leonid Kruglyak345, Mona Singh23 and Amy A Caudy3*

Author affiliations

1 Department of Molecular Biology, Princeton University, New Jersey, USA

2 Department of Computer Science, Princeton University, New Jersey, USA

3 Lewis-Sigler Institute of Integrative Genomics, Princeton University, New Jersey, USA

4 Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA

5 Howard Hughes Medical Institute, Princeton University, New Jersey, USA

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Citation and License

BMC Genomics 2009, 10:221  doi:10.1186/1471-2164-10-221

Published: 12 May 2009



High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.


Consequently, we compared full length cDNA sequencing to 2-channel gene expression microarrays in the context of measuring differential gene expression. Because of its comparable cost to a gene expression microarray, our study focused on the data obtainable from a single lane of an Illumina 1 G sequencer. We compared sequencing data to a highly replicated microarray experiment profiling two divergent strains of S. cerevisiae.


Using a large number of quantitative PCR (qPCR) assays, more than previous studies, we found that neither technology is decisively better at measuring differential gene expression. Further, we report sequencing results from a diploid hybrid of two strains of S. cerevisiae that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.