Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-channel Gene Expression Microarrays

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

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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • DNA, Complementary / genetics
  • DNA, Fungal / genetics
  • Gene Expression Profiling / methods*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Saccharomyces cerevisiae / genetics
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*

Substances

  • DNA, Complementary
  • DNA, Fungal