Research article

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

Joshua S Bloom^{* 1} , Zia Khan^{* 2} , Leonid Kruglyak^3,4,5 , Mona Singh^2,3 and Amy A Caudy³

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

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

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

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

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

author email corresponding author email* Contributed equally

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

Published:	12 May 2009

Abstract

Background

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.

Results

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.

Conclusion

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.