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BMC Genomics. 2009 May 12;10:221. doi: 10.1186/1471-2164-10-221.

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

Author information

1
Lewis-Sigler Institute of Integrative Genomics, Princeton University, New Jersey, USA. jbloom@princeton.edu

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.

PMID:
19435513
PMCID:
PMC2686739
DOI:
10.1186/1471-2164-10-221
[Indexed for MEDLINE]
Free PMC Article
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