Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene.
The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.
Thomassen
Mads
M
Department of Biochemistry, Pharmacology, and Genetics, Odense University Hospital and Human Microarray Centre, University of Southern Denmark, Odense, Denmark. mads.thomassen@ouh.fyns-amt.dk
Skov
Vibe
V
Eiriksdottir
Freyja
F
Tan
Qihua
Q
Jochumsen
Kirsten
K
Fritzner
Niels
N
Brusgaard
Klaus
K
Dahlgaard
Jesper
J
Kruse
Torben A
TA
D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020161:Physical Chromosome Mapping / Q000379:methods*