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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Hughes, TR; Mao, M; Jones, AR; Burchard, J; Marton, MJ; Shannon, KW; Lefkowitz, SM; Ziman, M; Schelter, JM; Meyer, MR; Kobayashi, S; Davis, C; Dai, H; He, YD; Stephaniants, SB; Cavet, G; Walker, WL; West, A; Coffey, E; Shoemaker, DD; Stoughton, R; Blanchard, AP; Friend, SH; Linsley, PS

Published Date

  • April 2001

Published In

Volume / Issue

  • 19 / 4

Start / End Page

  • 342 - 347

PubMed ID

  • 11283592

International Standard Serial Number (ISSN)

  • 1087-0156

Digital Object Identifier (DOI)

  • 10.1038/86730


  • eng

Conference Location

  • United States