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 language | English (US) |
|---|---|
| Pages (from-to) | 418-426 |
| Number of pages | 9 |
| Journal | Nature Biotechnology |
| Volume | 22 |
| Issue number | 4 |
| DOIs | |
| State | Published - Apr 1 2004 |
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ASJC Scopus subject areas
- Biotechnology
- Bioengineering
- Applied Microbiology and Biotechnology
- Molecular Medicine
- Biomedical Engineering
Cite this
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 journal › Article
}
TY - JOUR
T1 - Expression profiling using a hexamer-based universal microarray
AU - Roth, Matthew E.
AU - Feng, Li
AU - McConnell, Kevin J.
AU - Schaffer, Paul J.
AU - Guerra, Cesar E.
AU - Affourtit, Jason P.
AU - Piper, Kevin R.
AU - Guccione, Lorri
AU - Hariharan, Jayashree
AU - Ford, Maura J.
AU - Powell, Stephen W.
AU - Krishnaswamy, Harish
AU - Lane, Jennifer
AU - Guccione, Lisa
AU - Intrieri, Gino
AU - Merkel, Jane S.
AU - Perbost, Clotilde
AU - Valerio, Anthony
AU - Zolla, Brenda
AU - Graham, Carol D.
AU - Hnath, Jonathan
AU - Michaelson, Chris
AU - Wang, Rixin
AU - Ying, Baoge
AU - Halling, Conrad
AU - Parman, Craig E.
AU - Raha, Debasish
AU - Orr, Brent
AU - Jedrzkiewicz, Barbara
AU - Liao, Ji
AU - Tevelev, Anton
AU - Mattessich, Martin J.
AU - Kranz, David M
AU - Lacey, Michelle
AU - Kaufman, Joseph C.
AU - Kim, Junhyong
AU - Latimer, Darin R.
AU - Lizardi, Paul M.
PY - 2004/4/1
Y1 - 2004/4/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=11144354637&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=11144354637&partnerID=8YFLogxK
U2 - 10.1038/nbt948
DO - 10.1038/nbt948
M3 - Article
C2 - 15024387
AN - SCOPUS:11144354637
VL - 22
SP - 418
EP - 426
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 4
ER -