Direct calibration of PICKY-designed microarrays.
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 under the PICKY Download area.


CONCLUSIONS
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.
Chou
Hui-Hsien
HH
Department of Genetics, Development and Cell Biology and Department of Computer Science, Iowa State University, Ames, IA 50011, USA. hhchou@iastate.edu
Trisiriroj
Arunee
A
Park
Sunyoung
S
Hsing
Yue-Ie C
YI
Ronald
Pamela C
PC
Schnable
Patrick S
PS
D002138:Calibration; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000737:chemistry; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software
D018076:DNA, Complementary