Improving signal intensities for genes with low-expression on oligonucleotide microarrays
<p>Abstract</p> <p>Background</p> <p>DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hyb...
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doaj-316fc158fc944d969b2ca9edf9822f552020-11-25T00:29:20ZengBMCBMC Genomics1471-21642004-06-01513510.1186/1471-2164-5-35Improving signal intensities for genes with low-expression on oligonucleotide microarraysHu LimeiDunmire Valerie RTaylor Ellen EJia Jack YCogdell David ERamdas LathaHamilton Stanley RZhang Wei<p>Abstract</p> <p>Background</p> <p>DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested. We evaluated the effects of oligonucleotide probe length and concentration on signal intensity measurements of the expression levels of genes in a target sample.</p> <p>Results</p> <p>Selected genes of various expression levels in a single cell line were hybridized to oligonucleotide arrays of four lengths and four concentrations of probes to determine how these critical parameters affected the intensity of the signal representing their expression. We found that oligonucleotides of longer length significantly increased the signals of genes with low-expression in the target. High-expressing gene signals were also boosted but to a lesser degree. Increasing the probe concentration, however, did not linearly increase the signal intensity for either low- or high-expressing genes.</p> <p>Conclusions</p> <p>We conclude that the longer the oligonuclotide probe the better the signal intensities of low expressing genes on oligonucleotide arrays.</p> http://www.biomedcentral.com/1471-2164/5/35 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hu Limei Dunmire Valerie R Taylor Ellen E Jia Jack Y Cogdell David E Ramdas Latha Hamilton Stanley R Zhang Wei |
spellingShingle |
Hu Limei Dunmire Valerie R Taylor Ellen E Jia Jack Y Cogdell David E Ramdas Latha Hamilton Stanley R Zhang Wei Improving signal intensities for genes with low-expression on oligonucleotide microarrays BMC Genomics |
author_facet |
Hu Limei Dunmire Valerie R Taylor Ellen E Jia Jack Y Cogdell David E Ramdas Latha Hamilton Stanley R Zhang Wei |
author_sort |
Hu Limei |
title |
Improving signal intensities for genes with low-expression on oligonucleotide microarrays |
title_short |
Improving signal intensities for genes with low-expression on oligonucleotide microarrays |
title_full |
Improving signal intensities for genes with low-expression on oligonucleotide microarrays |
title_fullStr |
Improving signal intensities for genes with low-expression on oligonucleotide microarrays |
title_full_unstemmed |
Improving signal intensities for genes with low-expression on oligonucleotide microarrays |
title_sort |
improving signal intensities for genes with low-expression on oligonucleotide microarrays |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2004-06-01 |
description |
<p>Abstract</p> <p>Background</p> <p>DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested. We evaluated the effects of oligonucleotide probe length and concentration on signal intensity measurements of the expression levels of genes in a target sample.</p> <p>Results</p> <p>Selected genes of various expression levels in a single cell line were hybridized to oligonucleotide arrays of four lengths and four concentrations of probes to determine how these critical parameters affected the intensity of the signal representing their expression. We found that oligonucleotides of longer length significantly increased the signals of genes with low-expression in the target. High-expressing gene signals were also boosted but to a lesser degree. Increasing the probe concentration, however, did not linearly increase the signal intensity for either low- or high-expressing genes.</p> <p>Conclusions</p> <p>We conclude that the longer the oligonuclotide probe the better the signal intensities of low expressing genes on oligonucleotide arrays.</p> |
url |
http://www.biomedcentral.com/1471-2164/5/35 |
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