Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography
- Emile F. Nuwaysir1,
- Wei Huang2,
- Thomas J. Albert1,
- Jaz Singh1,
- Kate Nuwaysir1,
- Alan Pitas1,
- Todd Richmond1,
- Tom Gorski1,
- James P. Berg1,
- Jeff Ballin2,
- Mark McCormick1,
- Jason Norton1,
- Tim Pollock1,
- Terry Sumwalt1,
- Lawrence Butcher1,
- DeAnn Porter1,
- Michael Molla3,
- Christine Hall4,
- Fred Blattner5,
- Michael R. Sussman6,
- Rodney L. Wallace1,
- Franco Cerrina1,2, and
- Roland D. Green1,7
- 1NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA; 2Center for NanoTechnology, Department of Electrical Engineering and Computer Engineering, 3Computer Sciences Department, 4Department of Bacteriology, 5Department of Genetics, and 6Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA
Abstract
Microarrays containing 195,000 in situ synthesized oligonucleotide features have been created using a benchtop, maskless photolithographic instrument. This instrument, the Maskless Array Synthesizer (MAS), uses a digital light processor (DLP) developed by Texas Instruments. The DLP creates the patterns of UV light used in the light-directed synthesis of oligonucleotides. This digital mask eliminates the need for expensive and time-consuming chromium masks. In this report, we describe experiments in which we tested this maskless technology for DNA synthesis on glass surfaces. Parameters examined included deprotection rates, repetitive yields, and oligonucleotide length. Custom gene expression arrays were manufactured and hybridized toDrosophila melanogaster and mouse samples. Quantitative PCR was used to validate the gene expression data from the mouse arrays.
[The sequence data from this study have been submitted to GEO under accession nos. GPL208, GSM2409, GSM2410, GSM2411, GSM2412, GSM2413, GSM2414, GSE81, GSE82.]
Footnotes
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↵7 Corresponding author.
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E-MAIL rgreen{at}nimblegen.com; FAX (608) 218-7601.
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.362402.
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- Received April 16, 2002.
- Accepted September 10, 2002.
- Cold Spring Harbor Laboratory Press
