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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.

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