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Vol. 12, Issue 11, 1749-1755, November 2002

METHODS
Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography

Emile F. Nuwaysir,1 Wei Huang,2 Thomas J. Albert,1 Jaz Singh,1 Kate Nuwaysir,1 Alan Pitas,1 Todd Richmond,1 Tom Gorski,1 James P. Berg,1 Jeff Ballin,2 Mark McCormick,1 Jason Norton,1 Tim Pollock,1 Terry Sumwalt,1 Lawrence Butcher,1 DeAnn Porter,1 Michael Molla,3 Christine Hall,4 Fred Blattner,5 Michael R. Sussman,6 Rodney L. Wallace,1 Franco Cerrina,1,2 and Roland D. Green1,7

1 NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA; 2 Center for NanoTechnology, Department of Electrical Engineering and Computer Engineering, 3 Computer Sciences Department, 4 Department of Bacteriology, 5 Department of Genetics, and 6 Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA

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 to Drosophila 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.]

7 Corresponding author.

12:1749-1755 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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