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. Graham; Jonathan 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

doi:10.1038/nbt948

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

Biochemistry

Research output: Contribution to journal › Article › peer-review

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	https://doi.org/10.1038/nbt948
State	Published - Apr 2004

ASJC Scopus subject areas

Biotechnology
Bioengineering
Biomedical Engineering
Applied Microbiology and Biotechnology
Molecular Medicine

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10.1038/nbt948

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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

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

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title = "Expression profiling using a hexamer-based universal microarray",

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.",

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

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doi = "10.1038/nbt948",

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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.

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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.

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Expression profiling using a hexamer-based universal microarray

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