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Nucleic Acids Research Advance Access originally published online on January 10, 2008
Nucleic Acids Research 2008 36(4):1334-1342; doi:10.1093/nar/gkm1145
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1334-1342
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Microarray analysis using disiloxyl 70mer oligonucleotides

Marcus Gry Björklund1, Christian Natanaelsson1, Amelie Eriksson Karlström1, Yong Hao2 and Joakim Lundeberg1,*

1School of Biotechnology, Department of Gene Technology, KTH, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm and 2Oligovation, Dag Hammarskjölds väg 32 B, Uppsala Science Park, 751 83 Uppsala, Sweden

*To whom correspondence should be addressed. Tel: +46 8 553 8327; Fax: +46 8 553 78481; Email: joakim.lundeberg{at}biotech.kth.se

Received August 28, 2007. Revised November 18, 2007. Accepted December 10, 2007.

DNA microarray technology has evolved dramatically in recent years, and is now a common tool in researchers' portfolios. The scope of the technique has expanded from small-scale studies to extensive studies such as classification of disease states. Technical knowledge regarding solid phase microarrays has also increased, and the results acquired today are more reliable than those obtained just a few years ago. Nevertheless, there are various aspects of microarray analysis that could be improved. In this article we show that the proportions of full-length probes used significantly affects the results of global analyses of transcriptomes. In particular, measurements of transcripts in low abundance are more sensitive to truncated probes, which generally increase the degree of cross hybridization and loss of specific signals. In order to improve microarray analysis, we here introduce a disiloxyl purification step, which ensures that all the probes on the microarray are at full length. We demonstrate that when the features on microarrays consist of full-length probes the signal intensity is significantly increased. The overall increase in intensity enables the hybridization stringency to be increased, and thus enhance the robustness of the results.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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