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      Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

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          Abstract

          We 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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          Most cited references20

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          Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale

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            Light-directed, spatially addressable parallel chemical synthesis

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              Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation

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                Author and article information

                Journal
                Nature Biotechnology
                Nat Biotechnol
                Springer Science and Business Media LLC
                1087-0156
                1546-1696
                April 2001
                April 2001
                : 19
                : 4
                : 342-347
                Article
                10.1038/86730
                11283592
                de058c82-2463-4ae4-9e2b-12814698b63d
                © 2001

                http://www.springer.com/tdm

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