This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Paredes, C. J.
Right arrow Articles by Papoutsakis, E. T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Paredes, C. J.
Right arrow Articles by Papoutsakis, E. T.
Agricola
Right arrow Articles by Paredes, C. J.
Right arrow Articles by Papoutsakis, E. T.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, July 2007, p. 4631-4638, Vol. 73, No. 14
0099-2240/07/$08.00+0     doi:10.1128/AEM.00144-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum{triangledown} ,{dagger}

Carlos J. Paredes, Ryan S. Senger, Iwona S. Spath, Jacob R. Borden, Ryan Sillers, and Eleftherios T. Papoutsakis*

Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208

Received 19 January 2007/ Accepted 15 May 2007

While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.

* Corresponding author. Mailing address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208. Phone: (847) 491-7455. Fax: (847) 491-3728. E-mail: e-paps{at}northwestern.edu

{triangledown} Published ahead of print on 25 May 2007.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, July 2007, p. 4631-4638, Vol. 73, No. 14
0099-2240/07/$08.00+0     doi:10.1128/AEM.00144-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.





Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»