%0 Journal Article %J BMC Genomics %D 2009 %T Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays %A Bloom, Joshua S. %A Zia Khan %A Kruglyak, Leonid %A Singh, Mona %A Caudy, Amy A. %K Animal Genetics and Genomics %K Life Sciences, general %K Microarrays %K Microbial Genetics and Genomics %K Plant Genetics & Genomics %K proteomics %X 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. %B BMC Genomics %V 10 %P 1 - 10 %8 2009/12/01/ %@ 1471-2164 %G eng %U http://link.springer.com/article/10.1186/1471-2164-10-221 %N 1 %! BMC Genomics