Expression profiling using a hexamer-based universal microarray

Matthew E. Roth, Li Feng, Kevin J. McConnell, Paul J. Schaffer, Cesar E. Guerra, Jason P. Affourtit, Kevin R. Piper, Lorri Guccione, Jayashree Hariharan, Maura J. Ford, Stephen W. Powell, Harish Krishnaswamy, Jennifer Lane, Lisa Guccione, Gino Intrieri, Jane S. Merkel, Clotilde Perbost, Anthony Valerio, Brenda Zolla, Carol D. GrahamJonathan Hnath, Chris Michaelson, Rixin Wang, Baoge Ying, Conrad Halling, Craig E. Parman, Debasish Raha, Brent Orr, Barbara Jedrzkiewicz, Ji Liao, Anton Tevelev, Martin J. Mattessich, David M. Kranz, Michelle Lacey, Joseph C. Kaufman, Junhyong Kim, Darin R. Latimer, Paul M. Lizardi

Research output: Contribution to journalArticle

Abstract

We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific knowledge of transcript sequences. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (-80-120) of equal length DNA fragments. The resulting material is amplified and detected with the UMAS system, comprising all possible 4,096 (46) DNA hexamers. Ligation to the arrays yields thousands of 14-mer sequence tags. The compendium of signals from all pools in the array-of-universal arrays comprises a full-transcriptome expression profile. The technology was validated by analysis of the galactose response of Saccharomyces cerevisiae, and the resulting profiles showed excellent agreement with the literature and real-time PCR assays. The technology was also used to demonstrate expression profiling from a hybrid organism in a proof-of-concept experiment where a T-cell receptor gene was expressed in yeast.

Original languageEnglish (US)
Pages (from-to)418-426
Number of pages9
JournalNature Biotechnology
Volume22
Issue number4
DOIs
StatePublished - Apr 1 2004

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

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    Roth, M. E., Feng, L., McConnell, K. J., Schaffer, P. J., Guerra, C. E., Affourtit, J. P., Piper, K. R., Guccione, L., Hariharan, J., Ford, M. J., Powell, S. W., Krishnaswamy, H., Lane, J., Guccione, L., Intrieri, G., Merkel, J. S., Perbost, C., Valerio, A., Zolla, B., ... Lizardi, P. M. (2004). Expression profiling using a hexamer-based universal microarray. Nature Biotechnology, 22(4), 418-426. https://doi.org/10.1038/nbt948