TitleMeasuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.
Publication TypeJournal Article
Year of Publication2009
AuthorsBloom, JS, Khan, Z, Kruglyak, L, Singh, M, Caudy, AA
JournalBMC Genomics
Date Published2009
KeywordsAlgorithms, DNA, Complementary, DNA, Fungal, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Saccharomyces cerevisiae, Sequence Alignment, Sequence Analysis, DNA

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.

Alternate JournalBMC Genomics