@article {49749, title = {Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.}, journal = {BMC Genomics}, volume = {10}, year = {2009}, month = {2009}, pages = {221}, 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.

}, keywords = {algorithms, DNA, Complementary, DNA, Fungal, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Saccharomyces cerevisiae, sequence alignment, Sequence Analysis, DNA}, issn = {1471-2164}, doi = {10.1186/1471-2164-10-221}, author = {Bloom, Joshua S and Khan, Zia and Kruglyak, Leonid and Singh, Mona and Caudy, Amy A} }