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(Chest. 2002;121:80S.)
© 2002 American College of Chest Physicians

Use of Spotted Oligonucleotide Arrays for Large-Scale Analysis of Mammalian Gene Expression*

David J. Erle, MD; Laura Koth, MD; Oren Abramson, MD; Madeleine W. Rodriguez, BA and Andrea Barczak

* From the Functional Genomics Core Facility, UCSF Sandler Center for Basic Research in Asthma, University of California, San Francisco, San Francisco, CA.

Correspondence to: David J. Erle, MD, Associate Professor, Lung Biology Center, Box 0854, San Francisco, CA 94143-4123; e-mail: erle{at}itsa.ucsf.edu

A variety of technologies have been used to produce microarrays for the analysis of mammalian gene expression. Spotted complementary DNA arrays (produced by deposition of polymerase chain reaction products) and GeneChip oligonucleotide arrays (Affymetrix; Santa Clara, CA) [produced by in situ synthesis of oligonucleotides] have both been used successfully for this purpose, but these array technologies each have important limitations. In an attempt to overcome many of these limitations, we are employing an alternative approach based on the use of spotted oligonucleotide arrays. These arrays are being produced by depositing 70-mer oligonucleotides on modified glass slides. First-generation human arrays contain oligonucleotides corresponding to approximately 14,000 genes (one oligonucleotide per gene). We are optimizing methods for array production, postprocessing, production of labeled targets, hybridization, and data analysis. Our preliminary results indicate that spotted oligonucleotide arrays are an attractive alternative to other microarray technologies and may offer significant advantages in terms of cost, ease of production, flexibility, and specificity.




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