Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p>...
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doaj-79d63c70e00b4892848bc94b6159da3e2020-11-25T00:19:07ZengBMCBMC Genomics1471-21642009-05-0110122110.1186/1471-2164-10-221Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarraysKruglyak LeonidKhan ZiaBloom Joshua SSingh MonaCaudy Amy A<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>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 <it>S. cerevisiae </it>that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.</p> http://www.biomedcentral.com/1471-2164/10/221 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kruglyak Leonid Khan Zia Bloom Joshua S Singh Mona Caudy Amy A |
spellingShingle |
Kruglyak Leonid Khan Zia Bloom Joshua S Singh Mona Caudy Amy A Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays BMC Genomics |
author_facet |
Kruglyak Leonid Khan Zia Bloom Joshua S Singh Mona Caudy Amy A |
author_sort |
Kruglyak Leonid |
title |
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
title_short |
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
title_full |
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
title_fullStr |
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
title_full_unstemmed |
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
title_sort |
measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2009-05-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>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 <it>S. cerevisiae </it>that indicate full length cDNA sequencing can discover heterozygosity and measure quantitative allele-specific expression simultaneously.</p> |
url |
http://www.biomedcentral.com/1471-2164/10/221 |
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