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


CONCLUSIONS
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.
Lewis-Sigler Institute of Integrative Genomics, Princeton University, New Jersey, USA. jbloom@princeton.edu
Joshua S
JS
Bloom
Zia
Z
Khan
Leonid
L
Kruglyak
Mona
M
Singh
Amy A
AA
Caudy
D000465:Algorithms; D018076:DNA, Complementary / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
D018076:DNA, Complementary; D004271:DNA, Fungal