Methodology article

Direct calibration of PICKY-designed microarrays

Hui-Hsien Chou¹ , Arunee Trisiriroj² , Sunyoung Park³ , Yue-Ie C Hsing² , Pamela C Ronald⁴ and Patrick S Schnable⁵

¹Department of Genetics, Development and Cell Biology and Department of Computer Science, Iowa State University, Ames, IA 50011, USA

²Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan, Republic of China

³4000 S. Brahma Blvd. #E7, Kingsville, TX 78363, USA

⁴Department of Plant Pathology, University of California, Davis, CA 95616, USA

⁵Department of Agronomy, and Center for Plant Genomics, Plant Sciences Institute, Iowa State University, Ames, IA 50011, USA

author email corresponding author email

BMC Bioinformatics 2009, 10:347doi:10.1186/1471-2105-10-347

Published:	23 October 2009

Abstract

Background

Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples.

Results

Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu webcite under the PICKY Download area.

Conclusion

PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.