TY - JOUR T1 - Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays JF - BMC Genomics Y1 - 2009 A1 - Bloom, Joshua S. A1 - Zia Khan A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Caudy, Amy A. KW - Animal Genetics and Genomics KW - Life Sciences, general KW - Microarrays KW - Microbial Genetics and Genomics KW - Plant Genetics & Genomics KW - proteomics AB - 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. VL - 10 SN - 1471-2164 UR - http://link.springer.com/article/10.1186/1471-2164-10-221 CP - 1 J1 - BMC Genomics ER -