Expression profiling using a hexamer-based universal microarray

• Published in: Nature biotechnology Vol. 22; no. 4; pp. 418 - 426
• Main Authors: Parman, Craig E, Lizardi, Paul M, 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, 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
• Format: Journal Article
• Language: English
• Published: New York, NY Nature 01.04.2004; Nature Publishing Group
• Subjects: 3' Untranslated Regions; Algorithms; Animals; Arrays; Biological and medical sciences; Biotechnology; Deoxyribonucleic acid; Diverse techniques; DNA; DNA Fragmentation; DNA microarrays; DNA Restriction Enzymes - metabolism; DNA, Complementary - metabolism; Fundamental and applied biological sciences. Psychology; Galactose; Galactose - metabolism; Gene Expression Profiling - methods; Hexamers; Humans; Image Processing, Computer-Assisted; Lymphocytes T; Mice; Models, Genetic; Molecular and cellular biology; Muscle, Skeletal - metabolism; Muscles - metabolism; Nucleotide sequence; Oligonucleotide Array Sequence Analysis; Promoter Regions, Genetic; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - metabolism; Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Sequence Analysis, DNA; T cell receptors; T-Lymphocytes - metabolism; Technology assessment; Transcription; Transcriptomes; Transgenes; Yeasts; Fungi; Yeast; Transcription; Transcriptome; Ascomycetes; Technique; Gene expression; Saccharomyces cerevisiae; Thallophyta
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt948

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.