Expression profiling of microRNA using oligo DNA arrays

Methods

Volumn 44, Issue 1, 2008, Pages 22-30

  Liu, Chang Gong ^b   Spizzo, Riccardo ^a   Calin, George Adrian ^a   Croce, Carlo Maria ^b  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Cancer; Microarray; microRNA; Non coding RNA; Other diseases; Tumor profilling

Indexed keywords

DNA; MICRORNA; OLIGONUCLEOTIDE; UNTRANSLATED RNA;

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE TECHNOLOGY; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA ANALYSIS; RNA HYBRIDIZATION; RNA SEQUENCE;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 37349040713     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2007.10.010     Document Type: Article

References (79)

1. Waterston R.H., Lander E.S., and Sulston J.E. Proc. Natl. Acad. Sci. USA 99 (2002) 3712-3716
2. Lowe C.B., Bejerano G., and Haussler D. Proc. Natl. Acad. Sci. USA 104 (2007) 8005-8010
3. Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., and Haussler D. Science 304 (2004) 1321-1325
4. Costa F.F. Gene 357 (2005) 83-94
5. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Nature 391 (1998) 806-811
6. Lee R.C., Feinbaum R.L., and Ambros V. Cell 75 (1993) 843-854
7. Lau N.C., Lim L.P., Weinstein E.G., and Bartel D.P. Science 294 (2001) 858-862
8. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Science 294 (2001) 853-858
9. Nelson P.T., Baldwin D.A., Scearce L.M., Oberholtzer J.C., Tobias J.W., and Mourelatos Z. Nat. Methods 1 (2004) 155-161
10. Wang H., Ach R.A., and Curry B. RNA 13 (2007) 151-159
11. Tricoli J.V., and Jacobson J.W. Cancer Res. 67 (2007) 4553-4555
12. Lee R.C., and Ambros V. Science 294 (2001) 862-864
13. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., and Mello C.C. Cell 106 (2001) 23-34
14. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Science 294 (2001) 853-858
15. Schmittgen T.D., Jiang J., Liu Q., and Yang L. Nucleic Acids Res. 32 (2004) e43
16. Jiang J., Lee E.J., Gusev Y., and Schmittgen T.D. Nucleic Acids Res. 33 (2005) 5394-5403
17. Chen C., Ridzon D.A., Broomer A.J., Zhou Z., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., Lao K.Q., Livak K.J., and Guegler K.J. Nucleic Acids Res. 33 (2005) e179
18. Kloosterman W.P., Wienholds E., de Bruijn E., Kauppinen S., and Plasterk R.H. Nat. Methods 3 (2006) 27-29
19. Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., Downing J.R., Jacks T., Horvitz H.R., and Golub T.R. Nature 435 (2005) 834-838
20. Jones L. Trends Plant Sci. 7 (2002) 473-475
21. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., and Tuschl T. Curr. Biol. 12 (2002) 735-739
22. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., and Bartel D.P. Cell 110 (2002) 513-520
23. Ruby J.G., Jan C.H., and Bartel D.P. Nature 448 (2007) 83-86
24. Okamura K., Hagen J.W., Duan H., Tyler D.M., and Lai E.C. Cell 130 (2007) 89-100
25. Schena M., Shalon D., Davis R.W., and Brown P.O. Science 270 (1995) 467-470
26. Kreil D.P., Russell R.R., and Russell S. Methods Enzymol. 410 (2006) 73-98
27. Wolber P.K., Collins P.J., Lucas A.B., De Witte A., and Shannon K.W. Methods Enzymol. 410 (2006) 28-57
28. Dalma-Weiszhausz D.D., Warrington J., Tanimoto E.Y., and Miyada C.G. Methods Enzymol. 410 (2006) 3-28
29. Gershon D. Nature 437 (2005) 1195-1198
30. Hughes T.R., Hiley S.L., Saltzman A.L., Babak T., and Blencowe B.J. Methods Enzymol. 410 (2006) 300-316
31. Krichevsky A.M., King K.S., Donahue C.P., Khrapko K., and Kosik K.S. RNA 9 (2003) 1274-1781
32. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., Dumitru C.D., Shimizu M., Zupo S., Dono M., Alder H., Bullrich F., Negrini M., and Croce C.M. Proc. Natl. Acad. Sci. USA 101 (2004) 9740-9744
33. Castoldi M., Schmidt S., Benes V., Noerholm M., Kulozik A.E., Hentze M.W., and Muckenthaler M.U. RNA 12 (2006) 913-920
34. Michael M.Z., SM O.C., van Holst Pellekaan N.G., Young G.P., and James R.J. Mol. Cancer Res. 1 (2003) 882-891
35. Calin G.A., Ferracin M., Cimmino A., Di Leva G., Shimizu M., Wojcik S.E., Iorio M.V., Visone R., Sever N.I., Fabbri M., Iuliano R., Palumbo T., Pichiorri F., Roldo C., Garzon R., Sevignani C., Rassenti L., Alder H., Volinia S., Liu C.G., Kipps T.J., Negrini M., and Croce C.M. N. Engl. J. Med. 353 (2005) 1793-1801
36. Feinbaum R., and Ambros V. Dev. Biol. 210 (1999) 87-95
37. Houbaviy H.B., Murray M.F., and Sharp P.A. Dev. Cell 5 (2003) 351-358
38. Zhao Y., Ransom J.F., Li A., Vedantham V., von Drehle M., Muth A.N., Tsuchihashi T., McManus M.T., Schwartz R.J., and Srivastava D. Cell 129 (2007) 303-317
39. Suh M.R., Lee Y., Kim J.Y., Kim S.K., Moon S.H., Lee J.Y., Cha K.Y., Chung H.M., Yoon H.S., Moon S.Y., Kim V.N., and Kim K.S. Dev. Biol. 270 (2004) 488-498
40. Esau C., Kang X., Peralta E., Hanson E., Marcusson E.G., Ravichandran L.V., Sun Y., Koo S., Perera R.J., Jain R., Dean N.M., Freier S.M., Bennett C.F., Lollo B., and Griffey R. J. Biol. Chem. 279 (2004) 52361-52365
41. Georgantas III R.W., Hildreth R., Morisot S., Alder J., Liu C.G., Heimfeld S., Calin G.A., Croce C.M., and Civin C.I. Proc. Natl. Acad. Sci. USA 104 (2007) 2750-2755
42. Baroukh N., Ravier M.A., Loder M.K., Hill E.V., Bounacer A., Scharfmann R., Rutter G.A., and Van Obberghen E. J. Biol. Chem. 282 (2007) 19575-19588
43. Poy M.N., Eliasson L., Krutzfeldt J., Kuwajima S., Ma X., Macdonald P.E., Pfeffer S., Tuschl T., Rajewsky N., Rorsman P., and Stoffel M. Nature 432 (2004) 226-230
44. Esau C., Davis S., Murray S.F., Yu X.X., Pandey S.K., Pear M., Watts L., Booten S.L., Graham M., McKay R., Subramaniam A., Propp S., Lollo B.A., Freier S., Bennett C.F., Bhanot S., and Monia B.P. Cell Metab. 3 (2006) 87-98
45. Ashraf S.I., and Kunes S. Curr. Opin. Neurobiol. 16 (2006) 535-539
46. Calin G.A., Dumitru C.D., Shimizu M., Bichi R., Zupo S., Noch E., Aldler H., Rattan S., Keating M., Rai K., Rassenti L., Kipps T., Negrini M., Bullrich F., and Croce C.M. Proc. Natl. Acad. Sci. USA 99 (2002) 15524-15529
47. Takamizawa J., Konishi H., Yanagisawa K., Tomida S., Osada H., Endoh H., Harano T., Yatabe Y., Nagino M., Nimura Y., Mitsudomi T., and Takahashi T. Cancer Res. 64 (2004) 3753-3756
48. Yanaihara N., Caplen N., Bowman E., Seike M., Kumamoto K., Yi M., Stephens R.M., Okamoto A., Yokota J., Tanaka T., Calin G.A., Liu C.G., Croce C.M., and Harris C.C. Cancer Cell 9 (2006) 189-198
49. Iorio M.V., Ferracin M., Liu C.G., Veronese A., Spizzo R., Sabbioni S., Magri E., Pedriali M., Fabbri M., Campiglio M., Menard S., Palazzo J.P., Rosenberg A., Musiani P., Volinia S., Nenci I., Calin G.A., Querzoli P., Negrini M., and Croce C.M. Cancer Res. 65 (2005) 7065-7070
50. Bandres E., Cubedo E., Agirre X., Malumbres R., Zarate R., Ramirez N., Abajo A., Navarro A., Moreno I., Monzo M., and Garcia-Foncillas J. Mol. Cancer 5 (2006) 29
51. Ciafre S.A., Galardi S., Mangiola A., Ferracin M., Liu C.G., Sabatino G., Negrini M., Maira G., Croce C.M., and Farace M.G. Biochem. Biophys. Res. Commun. 334 (2005) 1351-1358
52. Calin G.A., and Croce C.M. Nat. Rev. Cancer 6 (2006) 857-866
53. Sugatani T., and Hruska K.A. J. Cell. Biochem. (2007)
54. O'Connell R.M., Taganov K.D., Boldin M.P., Cheng G., and Baltimore D. Proc. Natl. Acad. Sci. USA 104 (2007) 1604-1609
55. Thai T.H., Calado D.P., Casola S., Ansel K.M., Xiao C., Xue Y., Murphy A., Frendewey D., Valenzuela D., Kutok J.L., Schmidt-Supprian M., Rajewsky N., Yancopoulos G., Rao A., and Rajewsky K. Science 316 (2007) 604-608
56. Hayashita Y., Osada H., Tatematsu Y., Yamada H., Yanagisawa K., Tomida S., Yatabe Y., Kawahara K., Sekido Y., and Takahashi T. Cancer Res. 65 (2005) 9628-9632
57. Chan J.A., Krichevsky A.M., and Kosik K.S. Cancer Res. 65 (2005) 6029-6033
58. Cimmino A., Calin G.A., Fabbri M., Iorio M.V., Ferracin M., Shimizu M., Wojcik S.E., Aqeilan R.I., Zupo S., Dono M., Rassenti L., Alder H., Volinia S., Liu C.G., Kipps T.J., Negrini M., and Croce C.M. Proc. Natl. Acad. Sci. USA 102 (2005) 13944-13949
59. Ma L., Teruya-Feldstein J., and Weinberg R.A. Nature 449 (2007) 682-689
60. Costinean S., Zanesi N., Pekarsky Y., Tili E., Volinia S., Heerema N., and Croce C.M. Proc. Natl. Acad. Sci. USA 103 (2006) 7024-7029
61. Minino A.M., Heron M.P., Murphy S.L., and Kochanek K.D. Natl. Vital Stat. Rep. 55 (2007) 1-119
62. van Rooij E., Sutherland L.B., Liu N., Williams A.H., McAnally J., Gerard R.D., Richardson J.A., and Olson E.N. Proc. Natl. Acad. Sci. USA 103 (2006) 18255-18260
63. Lukiw W.J. Neuroreport 18 (2007) 297-300
64. Calin G.A., Liu C.G., Ferracin M., Hyslop T., Spizzo R., Sevignani C., Fabbri M., Cimmino A., Lee E.J., Wojcik S.E., Shimizu M., Tili E., Rossi S., Taccioli C., Pichiorri F., Liu X., Zupo S., Herlea V., Gramantieri L., Lanza G., Alder H., Rassenti L., Volinia S., Schmittgen T.D., Kipps T.J., Negrini M., and Croce C.M. Cancer Cell. 12 (2007) 215-229
65. Babak T., Zhang W., Morris Q., Blencowe B.J., and Hughes T.R. RNA 10 (2004) 1813-1819
66. Barad O., Meiri E., Avniel A., Aharonov R., Barzilai A., Bentwich I., Einav U., Gilad S., Hurban P., Karov Y., Lobenhofer E.K., Sharon E., Shiboleth Y.M., Shtutman M., Bentwich Z., and Einat P. Genome Res. 14 (2004) 2486-2494
67. Miska E.A., Alvarez-Saavedra E., Townsend M., Yoshii A., Sestan N., Rakic P., Constantine-Paton M., and Horvitz H.R. Genome Biol. 5 (2004) R68
68. Thomson J.M., Parker J., Perou C.M., and Hammond S.M. Nat. Methods 1 (2004) 47-53
69. Sun Y., Koo S., White N., Peralta E., Esau C., Dean N.M., and Perera R.J. Nucleic Acids Res. 32 (2004) e188
70. Baskerville S., and Bartel D.P. RNA 11 (2005) 241-247
71. Goff L.A., Yang M., Bowers J., Getts R.C., Padgett R.W., and Hart R.P. RNA Biol. 2 (2005)
72. Liang R.Q., Li W., Li Y., Tan C.Y., Li J.X., Jin Y.X., and Ruan K.C. Nucleic Acids Res 33 (2005) e17
73. Shingara J., Keiger K., Shelton J., Laosinchai-Wolf W., Powers P., Conrad R., Brown D., and Labourier E. Rna 11 (2005) 1461-1470
74. O'Donnell K.A., Wentzel E.A., Zeller K.I., Dang C.V., and Mendell J.T. Nature 435 (2005) 839-843
75. Fang S., Lee H.J., Wark A.W., and Corn R.M. J. Am. Chem. Soc. 128 (2006) 14044-14046
76. Mattie M.D., Benz C.C., Bowers J., Sensinger K., Wong L., Scott G.K., Fedele V., Ginzinger D., Getts R., and Haqq C. Mol. Cancer 5 (2006) 24
77. Beuvink I., Kolb F.A., Budach W., Garnier A., Lange J., Natt F., Dengler U., Hall J., Filipowicz W., and Weiler J. Nucleic Acids Res. 35 (2007) e52
78. Fan Y., Chen X., Trigg A.D., Tung C.H., Kong J., and Gao Z. J. Am. Chem. Soc. 129 (2007) 5437-5443
79. Liu Chang-Gong L.X., and Calin G.A. Bioinformatics. A Practical Approach (2008), Chapman & Hall/CRC Taylor & Francis