Nature Biotechnology
22, 418 - 426 (2004)
Published online: 14 March 2004; | doi:10.1038/nbt948
Expression profiling using a hexamer-based universal microarrayMatthew E Roth1, Li Feng1, 6, Kevin J McConnell1, 6, Paul J Schaffer1, 6, Cesar E Guerra1, 6, Jason P Affourtit1, 6, Kevin R Piper1, Lorri Guccione1, Jayashree Hariharan1, Maura J Ford1, Stephen W Powell1, Harish Krishnaswamy1, Jennifer Lane1, Lisa Guccione1, Gino Intrieri1, Jane S Merkel1, Clotilde Perbost1, Anthony Valerio1, Brenda Zolla1, Carol D Graham1, Jonathan Hnath1, Chris Michaelson1, Rixin Wang1, Baoge Ying1, Conrad Halling1, Craig E Parman1, Debasish Raha1, Brent Orr2, Barbara Jedrzkiewicz1, Ji Liao1, Anton Tevelev1, Martin J Mattessich1, David M Kranz2, Michelle Lacey3, Joseph C Kaufman1, Junhyong Kim4, Darin R Latimer1
& Paul M Lizardi51
Agilix Corporation, 2 Church Street South, New Haven, Connecticut, 06519, USA. 2
Department of Biochemistry, 322A RAL, University of Illinois, 600 S. Mathews, Urbana, Illinois 61801, USA. 3
Department of Statistics, 24 Hillhouse Avenue, Yale University, New Haven, Connecticut 06511, USA. 4
Department of Biology and Penn Center for Bioinformatics, 14th Floor, Blockley Hall, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6017, USA. 5
Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA. 6
These authors contributed equally to this work.
Correspondence should be addressed to Craig E Parman c.parman@agilixcorp.com or Paul M Lizardi paul.lizardi@yale.eduWe 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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