Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

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

For all author emails, please log on.

BMC Genomics 2009, 10:221  doi: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.