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A universal reference sample derived from clone vector for improved detection of differential gene expression

BACKGROUND: Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing si...

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Autores principales: Khan, Rishi L, Gonye, Gregory E, Gao, Guang, Schwaber, James S
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475850/
https://www.ncbi.nlm.nih.gov/pubmed/16677381
http://dx.doi.org/10.1186/1471-2164-7-109
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author Khan, Rishi L
Gonye, Gregory E
Gao, Guang
Schwaber, James S
author_facet Khan, Rishi L
Gonye, Gregory E
Gao, Guang
Schwaber, James S
author_sort Khan, Rishi L
collection PubMed
description BACKGROUND: Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs™. RESULTS: We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. CONCLUSION: Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes.
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spelling pubmed-14758502006-06-12 A universal reference sample derived from clone vector for improved detection of differential gene expression Khan, Rishi L Gonye, Gregory E Gao, Guang Schwaber, James S BMC Genomics Methodology Article BACKGROUND: Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs™. RESULTS: We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. CONCLUSION: Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes. BioMed Central 2006-05-05 /pmc/articles/PMC1475850/ /pubmed/16677381 http://dx.doi.org/10.1186/1471-2164-7-109 Text en Copyright © 2006 Khan et al; licensee BioMed Central Ltd.
spellingShingle Methodology Article
Khan, Rishi L
Gonye, Gregory E
Gao, Guang
Schwaber, James S
A universal reference sample derived from clone vector for improved detection of differential gene expression
title A universal reference sample derived from clone vector for improved detection of differential gene expression
title_full A universal reference sample derived from clone vector for improved detection of differential gene expression
title_fullStr A universal reference sample derived from clone vector for improved detection of differential gene expression
title_full_unstemmed A universal reference sample derived from clone vector for improved detection of differential gene expression
title_short A universal reference sample derived from clone vector for improved detection of differential gene expression
title_sort universal reference sample derived from clone vector for improved detection of differential gene expression
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1475850/
https://www.ncbi.nlm.nih.gov/pubmed/16677381
http://dx.doi.org/10.1186/1471-2164-7-109
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