Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis

Nature Methods

Volumn 1, Issue 3, 2004, Pages 241-248

  Cleary, Michele A ^a   Kilian, Kristopher ^a   Wang, Yanqun ^a   Bradshaw, Jeff ^a   Cavet, Guy ^a   Ge, Wei ^a   Kulkarni, Amit ^a   Paddison, Patrick J ^b   Chang, Kenneth ^b   Sheth, Nihar ^b   Leproust, Eric ^c   Coffey, Ernest M ^a   Burchard, Julja ^a   McCombie, W Richard ^b   Linsley, Peter ^a   Hannon, Gregory J ^b  

^a ROSETTA INPHARMATICS   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c AGILENT TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ANIMAL; ARTICLE; CHEMISTRY; COMPUTER; DNA MICROARRAY; EVALUATION; GENETICS; HUMAN; IN SITU HYBRIDIZATION; METHODOLOGY; MOLECULAR CLONING; MOUSE; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION;

ANIMALS; CLONING, MOLECULAR; COMPUTER PERIPHERALS; HUMANS; IN SITU HYBRIDIZATION; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; RNA;

EID: 20844438492     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth724     Document Type: Article

References (33)

1. Hudson, J.D. et al. A proinflammatory cytokine inhibits p53 tumor suppressor activity. J. Exp. Med. 190, 1375-1382 (1999).
2. Brummelkamp, T.R. et al. TBX-3, the gene mutated in Ulnar-Mammary Syndrome, is a negative regulator of p19ARF and inhibits senescence. J. Biol. Chem. 277, 6567-6572 (2002).
3. Maestro, R. et al. Twist is a potential oncogene that inhibits apoptosis. Genes Dev. 13, 2207-2217 (1999).
4. Raveh, T., Berissi, H., Eisenstein, M., Spivak, T. & Kimchi, A. A functional genetic screen identifies regions at the C-terminal tail and death-domain of death-associated protein kinase that are critical for its proapoptotic activity. Proc. Natl. Acad. Sci. USA 97, 1572-1577 (2000).
5. Fletcher, B.S., Dragstedt, C., Notterpek, L. & Nolan, G.P. Functional cloning of SPIN-2, a nuclear anti-apoptotic protein with roles in cell cycle progression. Leukemia 16, 1507-1518 (2002).
6. Rayner, J.R. & Gonda, T.J. A simple and efficient procedure for generating stable expression libraries by cDNA cloning in a retroviral vector. Mol. Cell. Biol.14, 880-887 (1994).
7. Kitamura, T. et al. Efficient screening of retroviral cDNA expression libraries. Proc. Natl. Acad. Sci. USA 92, 9146-9150 (1995).
8. Kojima, T. & Kitamura, T. A signal sequence trap based on a constitutively active cytokine receptor. Nat. Biotechnol. 17, 487-490 (1999).
9. Golovkina, T.V. et al. A novel membrane protein is a mouse mammary tumor virus receptor. J. Virol. 72, 3066-3071 (1998).
10. Battini, J.L., Rasko, J.E. & Miller, A.D. A human cell-surface receptor for xenotropic and polytropic murine leukemia viruses: Possible role in G protein-coupled signal transduction. Proc. Natl. Acad. Sci. USA 96, 1385-1390 (1999).
11. Gallagher, W.M., Cairney, M., Schott, B., Roninson, I.B. & Brown, R. Identification of p53 genetic suppressor elements which confer resistance to cisplatin. Oncogene 14, 185-193 (1997).
12. Garkavtsev, I., Kazarov, A., Gudkov, A. & Riabowol, K. Suppression of the novel growth inhibitor p33ING1 promotes neoplastic transformation. Nat. Genet. 14, 415-420 (1996).
13. Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H. & Toole, J.J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355, 564-566 (1992).
14. Tuerk, C., MacDougal, S. & Gold, L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 89, 6988-6992 (1992).
15. Hughes, T.R. et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol 19, 342-347 (2001).
16. Hahiwell, C. & Cass, A.E. A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces. Anal. Chem. 73, 2476-2483 (2001).
17. Brown, D.M. A brief history of oligonucleotide synthesis. Methods Mol. Biol. 20, 1-17 (1993).
18. Bourdeiu, L., Silberzan, P. & Chatenay, D. Langmuir-Blodgett films: From micron to angstrom. Physical Review Letters 7, 2029-2032 (1991).
19. LeProust, E., Zhang, H., Yu, P., Zhou, X. & Gao, X. Characterization of oligodeoxyribonucleotide synthesis on glass plates. Nucleic Acids Res. 29, 2171-2180 (2001).
20. Hannon, G.J. & Rossi, J.J. Unlocking the potential of the human genome with RNA interference. Nature 431, 371-378 (2004).
21. Brummelkamp, T.R., Bernards, R. & Agami, R. A System for Stable Expression of Short Interfering RNAs in Mammalian Cells. Science 296, 550-553 (2002).
22. Paddison, P.J., Caudy, A.A., Bernstein, E., Hannon, G.J. & Conklin, D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16, 948-958 (2002).
23. Paul, C.P., Good, P.D., Winer, I. & EngeLke, D.R. Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20, 505-508 (2002).
24. Lee, N.S. et al. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat. Biotechnol. 20, 500-505 (2002).
25. Sui, G. et al. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 5515-5520 (2002).
26. Kawasaki, H. & Taira, K. Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells. Nucleic Acids Res. 31, 700-707 (2003).
27. Miyagishi, M. & Taira, K. U6 promoter-driven siRNAs with four uridine 3’ overhangs efficiently suppress targeted gene expression in mammalian cells. Nat. Biotechnol. 20, 497-500 (2002).
28. Paddison, P.J. A resource for Large-scale RNA-interference-based screens in mammals. Nature 428, 427-431 (2004).
29. Berns, K. et al. A Large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431-437 (2004).
30. Sen, G., Wehrman, T.S., Myers, J.W. & BLau, H.M. Restriction enzyme-generated siRNA (REGS) vectors and Libraries. Nat. Genet. 36, 183-189 (2004).
31. Shirane, D. et al. Enzymatic production of RNAi Libraries from cDNAs. Nat. Genet. 36, 190-196 (2004).
32. Luo, B., Heard, A.D. & Lodish, H.F. Small interfering RNA production by enzymatic engineering of DNA (SPEED). Proc. Natl. Acad. Sci. USA 101, 5494-5499 (2004).
33. Hsieh, A.C. et al. A Library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: Determinants of gene silencing for use in cell-based screens. Nucleic Acids Res. 32, 893-901 (2004).