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Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays
Open accessAbstract
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.
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Metadata
- Authors
- Bloom, J. S., Khan, Z., Kruglyak, L., Singh, M., & Caudy, A. A.
- Venue
- BMC Genomics
- Published
- 2009-05-12
- Volume
- 10
- Issue
- 1
- Pages
- 221-221
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W1973838650
- Cited by
- 180
- References
- 4
- FWCI
- 8.52
- Type
- journal article
- Language
- en
- Open access
- gold
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