|Title||Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.|
|Publication Type||Journal Article|
|Year of Publication||2009|
|Authors||Bloom, JS, Khan, Z, Kruglyak, L, Singh, M, Caudy, AA|
|Keywords||Algorithms, 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 Journal||BMC Genomics|