Published online before print
June 12, 2003
Genome Research, DOI: 10.1101/gr.1048803
Methods
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
Andrea Barczak1,
Madeleine Willkom Rodriguez1,
Kristina Hanspers2,
Laura L. Koth1,
Yu Chuan Tai3,
Benjamin M. Bolstad3,
Terence P. Speed4,5 and
David J. Erle1,6
1 Department of Medicine, University of California, San Francisco, San
Francisco, California 94143, USA
,
2 Gladstone Institute of Cardiovascular Disease, San Francisco, California
94141, USA
,
3 Group in Biostatistics, University of California, Berkeley, California
94720, USA
,
4 Department of Statistics, University of California, Berkeley, California
94720, USA
,
5 Division of Genetics and Bioinformatics, The Walter and Eliza Hall
Institute of Medical Research, Parkville, Vic 3050, Australia
DNA microarrays produced by deposition (or `spotting') of a single long
oligonucleotide probe for each gene may be an attractive alternative to other
types of arrays. We produced spotted oligonucleotide arrays using two large
collections of  70-mer probes, and used these arrays to analyze gene
expression in two dissimilar human RNA samples. These samples were also
analyzed using arrays produced by in situ synthesis of sets of multiple short
(25-mer) oligonucleotides for each gene (Affymetrix GeneChips). We compared
expression measurements for 7344 genes that were represented in both long
oligonucleotide probe collections and the in situ-synthesized 25-mer arrays.
We found strong correlations (r = 0.8–0.9) between relative
gene expression measurements made with spotted long oligonucleotide probes and
in situ-synthesized 25-mer probe sets. Spotted long oligonucleotide arrays
were suitable for use with both unamplified cDNA and amplified RNA targets,
and are a cost-effective alternative for many functional genomics
applications. Most previously reported evaluations of microarray technologies
have focused on expression measurements made on a relatively small number of
genes. The approach described here involves far more gene expression
measurements and provides a useful method for comparing existing and emerging
techniques for genome-scale expression analysis.
[Data from this study are available from GEO
(http://www.ncbi.nlm.nih.gov/geo) and are listed under the following accession
numbers: GSE344 (for the entire experimental series), GSM4843-GSM4865 (for the
expression data from individual arrays), and GPL91, GPL273, and GPL274 (for
the three array platforms).]
6 Corresponding author.
E-MAIL
erle{at}itsa.ucsf.edu;
FAX (415) 206-4123.
Article and publication are at
http://www.genome.org/cgi/doi/10.1101/gr.1048803. Article published online
before print in June 2003.
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