Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (371K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
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 Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Drobyshev, A. L.
Right arrow Articles by Beckers, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Drobyshev, A. L.
Right arrow Articles by Beckers, J.
Related Collections
Right arrow Microarray
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 2 e1
© 2003 Oxford University Press

Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies

Alexei L. Drobyshev, Christine Machka, Marion Horsch, Matthias Seltmann, Volkmar Liebscher1, Martin Hrabé de Angelis and Johannes Beckers*

Institute of Experimental Genetics and 1 Institute of Biomathematics and Biometry, GSF–National Research Centre for Environment and Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany

*To whom correspondence should be addressed. Tel: +49 89 3187 3513; Fax: +49 89 3187 3500; Email: beckers{at}gsf.de

The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the specificity of hybridisation. SAFE (specificity assessment from fractionation experiments) is a novel method to discriminate between non- specific cross-hybridisation and specific signals. We applied in situ fractionation of hybridised target on DNA-chips by means of repeated washes with increasing stringencies. Different fractions of hybridised target are washed off at defined stringencies and the collected fluorescence intensity data at each step comprise the fractionation curve. Based on characteristic features of the fractionation curve, unreliable data can be filtered and eliminated from subsequent analyses. The approach described here provides a novel experimental tool to identify probes that produce specific hybridisation signals in DNA-chip expression profiling approaches. The iterative use of the SAFE procedure will result in increasingly reliable sets of probes for microarray experiments and significantly improve the overall efficiency and reliability of RNA expression profiling data from DNA-chip experiments.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Physiol. GenomicsHome page
B. H. Mecham, D. Z. Wetmore, Z. Szallasi, Y. Sadovsky, I. Kohane, and T. J. Mariani
Increased measurement accuracy for sequence-verified microarray probes
Physiol Genomics, August 11, 2004; 18(3): 308 - 315.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.