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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
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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 (approximately 80-120) of equal length DNA fragments. The resulting material is amplified and detected with the UMAS system, comprising all possible 4,096 (4(6)) 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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3' Untranslated RegionsAlgorithmsAnimalsDNA FragmentationDNA Restriction EnzymesDNA, ComplementaryGalactoseGene Expression ProfilingHumansImage Processing, Computer-AssistedMiceModels, GeneticMuscle, SkeletalMusclesOligonucleotide Array Sequence AnalysisPromoter Regions, GeneticRNA, MessengerReverse Transcriptase Polymerase Chain ReactionSaccharomyces cerevisiaeSequence Analysis, DNAT-LymphocytesTransgenesJournal Article

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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. 2004-03-14. Expression profiling using a hexamer-based universal microarray.. https://doi.org/10.1038/nbt948

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