Nature Biotechnology
19, 342 - 347 (2001)
doi:10.1038/86730
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizerTimothy R. Hughes1, Mao Mao1, Allan R. Jones1, Julja Burchard1, Matthew J. Marton1, Karen W. Shannon2, Steven M. Lefkowitz2, Michael Ziman1, Janell M. Schelter1, Michael R. Meyer1, Sumire Kobayashi1, Colleen Davis1, Hongyue Dai1, Yudong D. He1, Sergey B. Stephaniants1, Guy Cavet1, Wynn L. Walker1, Anne West1, Ernest Coffey1, Daniel D. Shoemaker1, Roland Stoughton1, Alan P. Blanchard1, Stephen H. Friend1
& Peter S. Linsley11
Rosetta Inpharmatics, Inc., 12040 115th Avenue NE, Kirkland, WA 98034. 2
Agilent Technologies, Inc., 3500 Deer Creek Road, Palo Alto, CA 94304.
Correspondence should be addressed to Peter S. Linsley plinsley@rii.comWe describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.
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