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

Fingerprint

Microarrays
Transcriptome
Yeast
DNA
Technology
T-Cell Receptor Genes
T-cells
DNA Restriction Enzymes
T-Cell Antigen Receptor
Galactose
Ligation
Saccharomyces cerevisiae
Real-Time Polymerase Chain Reaction
Assays
Complementary DNA
Genes
Yeasts
Experiments
Endonucleases

ASJC Scopus subject areas

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

Cite this

Roth, M. E., Feng, L., McConnell, K. J., Schaffer, P. J., Guerra, C. E., Affourtit, J. P., ... Lizardi, P. M. (2004). Expression profiling using a hexamer-based universal microarray. Nature Biotechnology, 22(4), 418-426. https://doi.org/10.1038/nbt948

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

In: Nature Biotechnology, Vol. 22, No. 4, 01.04.2004, p. 418-426.

Research output: Contribution to journalArticle

Roth, ME, Feng, L, McConnell, KJ, Schaffer, PJ, Guerra, CE, Affourtit, JP, Piper, KR, Guccione, L, Hariharan, J, Ford, MJ, Powell, SW, Krishnaswamy, H, Lane, J, Guccione, L, Intrieri, G, Merkel, JS, Perbost, C, Valerio, A, Zolla, B, Graham, CD, Hnath, J, Michaelson, C, Wang, R, Ying, B, Halling, C, Parman, CE, Raha, D, Orr, B, Jedrzkiewicz, B, Liao, J, Tevelev, A, Mattessich, MJ, Kranz, DM, Lacey, M, Kaufman, JC, Kim, J, Latimer, DR & Lizardi, PM 2004, 'Expression profiling using a hexamer-based universal microarray', Nature Biotechnology, vol. 22, no. 4, pp. 418-426. https://doi.org/10.1038/nbt948
Roth ME, Feng L, McConnell KJ, Schaffer PJ, Guerra CE, Affourtit JP et al. Expression profiling using a hexamer-based universal microarray. Nature Biotechnology. 2004 Apr 1;22(4):418-426. https://doi.org/10.1038/nbt948
Roth, Matthew E. ; Feng, Li ; McConnell, Kevin J. ; Schaffer, Paul J. ; Guerra, Cesar E. ; Affourtit, Jason P. ; Piper, Kevin R. ; Guccione, Lorri ; Hariharan, Jayashree ; Ford, Maura J. ; Powell, Stephen W. ; Krishnaswamy, Harish ; Lane, Jennifer ; Guccione, Lisa ; Intrieri, Gino ; Merkel, Jane S. ; Perbost, Clotilde ; Valerio, Anthony ; Zolla, Brenda ; Graham, Carol D. ; Hnath, Jonathan ; Michaelson, Chris ; Wang, Rixin ; Ying, Baoge ; Halling, Conrad ; Parman, Craig E. ; Raha, Debasish ; Orr, Brent ; Jedrzkiewicz, Barbara ; Liao, Ji ; Tevelev, Anton ; Mattessich, Martin J. ; Kranz, David M ; Lacey, Michelle ; Kaufman, Joseph C. ; Kim, Junhyong ; Latimer, Darin R. ; Lizardi, Paul M. / Expression profiling using a hexamer-based universal microarray. In: Nature Biotechnology. 2004 ; Vol. 22, No. 4. pp. 418-426.
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