Expression profiling using a hexamer-based universal microarray

Nature Biotechnology

Volumn 22, Issue 4, 2004, Pages 418-426

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

^a Agilix Corp   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c YALE UNIVERSITY   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

^e YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; DNA; ENZYMES; REAL TIME SYSTEMS; SUGARS; YEAST;

ENZYMATIC MANIPULATIONS; UNIVERSAL MICRO ARRAY SYSTEMS (UMAS);

GENETIC ENGINEERING;

BIOTIN; COMPLEMENTARY DNA; DNA; DNA FRAGMENT; GALACTOSE; HEMAGGLUTININ; OLIGONUCLEOTIDE; RESTRICTION ENDONUCLEASE; RNA; STREPTAVIDIN; T LYMPHOCYTE RECEPTOR;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMPLICON; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SIGNAL PROCESSING; SPECIES DIFFERENCE;

3' UNTRANSLATED REGIONS; ALGORITHMS; ANIMALS; DNA FRAGMENTATION; DNA RESTRICTION ENZYMES; DNA, COMPLEMENTARY; GALACTOSE; GENE EXPRESSION PROFILING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICE; MODELS, GENETIC; MUSCLE, SKELETAL; MUSCLES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, DNA; T-LYMPHOCYTES; TRANSGENES;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 11144354637     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt948     Document Type: Article

References (42)

1. Janssen, P. et al. Beyond 100 Genomes. Genome Biol. 4, 402 (2003).
2. Liang, P. & Pardee, A. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967-971 (1992).
3. Saha, S. et al. Using the transcriptome to annotate the genome. Nat. Biotechnol. 19, 508-512 (2002).
4. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484-487 (1995).
5. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634 (2000).
6. Brenner, S. et al. In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc. Natl. Acad. Sci. USA 97, 1665-1670 (2000).
7. Sutcliffe, J.G. et al. TOGA: An automated parsing technology for analyzing expression on nearly all genes. Proc. Natl. Acad. Sci. USA 97, 1976-1981 (2002).
8. Shimkets, R.A. et al. Gene expression analysis by transcript profiling coupled to a gene database query. Nat. Biotechnol. 17, 798-803 (1999).
9. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
10. Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotides arrays. Nat. Biotechnol. 14, 1675-1680 (1996).
11. Ramakrishnan, R. et al. An assessment of Motorola codelink microarray performance for expression profiling applications. Nucleic Acids Res. 30, e30, (2002).
12. Hughes, T.R. et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotides synthesizer. Nat. Biotechnol. 19, 342-347 (2001).
13. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
14. van Dam, R.M. & Quake, S.R. Gene expression analysis with universal n-mer array. Genome Res. 12, 145-152 (2002).
15. Housby, J.N. & Southern, E.M. Fidelity of DNA ligation: a novel experimental approach based on the polymerization of libraries of oligonucleotides. Nucleic Acids Res. 26, 4259-4266 (1998).
16. Prichard, C.E. & Southern, E.M. Effects of base mismatches on joining of short oligodeoxynulceotides by DNA ligases. Nucleic Acids Res. 25, 3403-3407 (1997).
17. Cherepanov, A., Yildirim, E. & de Vries, S. Joining of short DNA oligonucleotides with base pair mismatches by T4 DNA ligase. J. Biochem. 129, 61-68 (2001).
18. James, K.D., Boles, A.R., Henckel, D. & Ellington, A.D. The fidelity of template-directed oligonucleotides ligation and its relevance to DNA computation. Nucleic Acids Res. 26, 5203-5211 (1998).
19. James, K.D. & Ellington, A.D. Surprising fidelity of template-directed chemical ligation of oligonucleotides. Chem. Biol. 4, 595-605 (1997).
20. Rossi, R., Montecucco, A., Ciarrocchi, G. & Biamonti, G. Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action. Nucleic Acids Res. 25, 2106-2113 (1997).
21. Aoi, Y., Yoshinobu, T., Tanizawa, K., Kinoshita, K. & Iwasaki, H. Ligation errors in DNA computing. Biosystems 52, 181-187 (1999).
22. Faulhammer, D., Lipton, R.J. & Landweber, L.F. Fidelity of enzymatic ligation for DNA computing. J. Comput. Bio. 7, 839-848 (2000).
23. Breslauer, K.J., Frank, R., Blocker, H. & Marky, L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746-3750 (1986).
24. Frierer, S.M. et al. Improved free-energy parameters for prediction of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83, 9373-9377 (1986).
25. SantaLucia, J. Jr. A unified view of polymer, dumbbell, and oligonucleotides DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465 (1998).
26. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
27. Roth, F.P., Hughes, J.D., Estep, P.W. & Church, G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939-945 (1998).
28. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
29. Oshiro, G. et al. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res. 12, 1210-1220 (2002).
30. Kumar, A. et al. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20, 58-63 (2002).
31. Velculescu, V.E. et al. Characterization of the yeast transcriptome. Cell 88, 243-251 (1997).
32. Martin, V.J.J., Pitera, D.J., Withers, S.T., Newman, J.D. & Keasling, J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796-802 (2003).
33. Szczebara, F.M. et al. Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nat. Biotechnol. 21, 143-149 (2003).
34. Boder, E.T. & Wittrup, K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553-557 (1997).
35. Holler, P.D. et al. In vitro evolution of a T-cell receptor with high affinity for peptide/MHC. Proc. Natl. Acad. Sci. USA 97, 5387-5392 (2000).
36. Sasik, R., Calvo, E. & Corbeil, J. Statistical analysis of high-density oligonucleotides arrays: a multiplicative noise model. Bioinformatics 18, 1633-1640 (2002).
37. Rinn, J.L. et al. The transcriptional activity of human chromosome 22. Gen. & Dev. 17, 529-540.
38. Baug, L.R., Hill, A.A., Brown, E.L. & Hunter, C. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29, e29 (2001).
39. Demers, L.M. et al. Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography. Science 296, 1836-1838 (2002).
40. Park, S.J., Taton, T.A. & Mirkin, C.A. Array-based electrical detection of DNA with nanoparticle probes. Science 295, 1503-1506 (2002).
41. Edgar, R., Domrachev, M. & Lash, A.E. Gene Expression Omnibus: NCBI gene and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
42. Zhao, J., Hyman, L., Moore, C. & Smith, T.F. Genomic detection of new yeast pre-mRNA 3-end processing. Nucleic Acids Res. 27, 888-894 (1999).