SuperSAGE: A modern platform for genome-wide quantitative transcript profiling

Current Pharmaceutical Biotechnology

Volumn 9, Issue 5, 2008, Pages 368-374

  Matsumura, Hideo ^a   Krüger, Detlev H ^b   Kahl, Günter ^c,d   Terauchi, Ryohei ^a  

^a IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c GOETHE UNIVERSITY   (Germany)

^d GENXPRO GMBH   (Germany)

Author keywords

Interaction transcriptome; Microarray; Next Generation Sequencing; Non model organism; SuperSAGE; SuperSAGE array; Transcriptome

Indexed keywords

COMPLEMENTARY DNA; DNA FRAGMENT; NUCLEOTIDE; TRANSCRIPTOME; PROTEOME; TRANSCRIPTION FACTOR;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ANALYTIC METHOD; AUTOMATION; BIOINFORMATICS; BIOTECHNOLOGY; COMPUTER MODEL; COMPUTER PROGRAM; DATA ANALYSIS; DNA DETERMINATION; DNA EXTRACTION; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; EUKARYOTE; FUNCTIONAL GENOMICS; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENOME; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HISTOPATHOLOGY; HOST PATHOGEN INTERACTION; METHODOLOGY; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PLANT GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PYROSEQUENCING; QUANTITATIVE TRAIT LOCUS; RESTRICTION MAPPING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SERIAL ANALYSIS OF GENE EXPRESSION; BIOLOGY; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; METABOLISM;

EUKARYOTA;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; TRANSCRIPTION FACTORS;

EID: 58149293709     PISSN: 13892010     EISSN: 18734316     Source Type: Journal    
DOI: 10.2174/138920108785915157     Document Type: Review

References (26)

1. Schena, M.; Shalon, D.; Davis, R. W. and Brown, P. Q. (1995) Science, 270, 467-470.
2. Velculescu, V. E.; Zhang, L.; Vogelstein, B. and Kinzler, K.W. (1995) Science, 270, 484-487.
3. Matsumura, H.; Nirasawa, S. and Terauchi, R. (1999) Plant J., 20, 719-726.
4. Fregene, M.; Matsumura, H.; Akano, A.; Dixon, A. and Terauchi, R. (2004) Plant Mol. Biol., 56, 563-571.
5. van den Berg, A.; van der Leij, J. and Poppema S. (1999) Nucleic Acids Res., 27, e17.
6. Chen, J.J.; Rowley, J.D. and Wang, S.M. (2000) Proc. Natl. Acad. Sci. USA, 97, 349-53.
7. Polyak, K.; Xia, Y.; Zweier, J. L.; Kinzler, K.; W. and Vogelstein, B. (1997) Nature, 389, 300-305
8. Saha, S.; Sparks, A; B.;Rago, C.; Akmaev, V.; Wang, C. J.; Vogelstein, B.; Kinzler, K. W. and Velculescu, V. E. (2002) Nat. Biotechnol., 20, 508-512.
9. Matsumura, H.; Reich, S.; Ito, A.; Saitoh, H.; Kamoun, S.; Winter, P.; Kahl, G..; Reuter, M.; Krüger, D. H. and Terauchi, R. (2003) Proc. Natl. Acad. Sci. USA, 100, 15718-15723.
10. Mücke, M.; Reich, S.; Möncke-Buchner, E.; Reuter, M. and Krüger D.H. (2001) J. Mol. Biol., 312, 687-98.
11. Sears, A.; Peakman, L.J.; Wilson, G.G. and Szczelkun, M.D. (2005) Nucleic Acids Res., 33, 4775-87.
12. Möncke-Buchner, E.; Mackeldanz, P.; Krüger, D.H. and Reuter, M. (2004) J. Biotechnol., 114, 99-106.
13. Matsumura, H.; Reich, S.; Reuter, M.; Kruger, D. H.; Winter, P.; Kahl, G. and Terauchi, R. (2004) in SAGE: Current Technologies and Application, (Wang, S. M., Ed.), Horizon Scientific Press, Norwich, UK, pp. 77-90.
14. Matsumura, H.; Reuter, M.; Kruger, D. H.; Winter, P.; Kahl, G. and Terauchi, R. (2008) in Methods in Molecular Biology, Vol. 387, (Nielsen K.L., Ed.), Humana Press, Totowa, NJ, pp. 55-70.
15. Terauchi, R.; Matsumura, H.; Krüger, D.H. and Kahl, G. (2008).in The Handbook of Functional Genomics, (Kahl G.; Meksem K. Eds.), Wiley-VCH Publ., Weinheim-Berlin, in press.
16. Matsumura, H.; Ito, A.; Saitoh, H.; Winter, P.; Kahl, G.; Reuter, M.; Kruger, D. H. and Terauchi, R. (2004) Cell. Microbiol., 7, 11-18.
17. Bin Nasir, K.; H.; Takahashi.; Y.; Ito, A.; Saitoh.; H.; Matsumura, H.; Kanzaki, H.; Shimizu, T.; Ito, M..; Sharma, P.; C.; Ohme-Takagi, M.; Kamoun, S. and Terauhi, R. (2005) Plant J., 43, 491-505.
18. Matsumura, H.; Bin Nasir, K. H.; Yoshida, K.; Ito, A.; Kahl, G.; Krüger, D. H. and Terauchi, R. (2006) Nat. Methods, 3, 469-474.
19. Coemans, B.; Matsumura, H.; Terauchi, R.; Remy, S; Swennen, R. and Sagi, L. (2005) Theor. Appl. Genet, 111, 1118-1126
20. Ohtsu, K.; Takahashi, H.; Schnable, P.S. and Nakazono, M. (2007) Plant Cell Physiol., 48, 3-7.
21. Terauchi, R.;Win, J.; Kamoun, S.; Matsumura, H.;Saitoh, H.; Yoshida, K.; Fujisawa, S.; Shenton, M.; Berberich, T.; Ito, A.; Takano, Y. and Tosa, Y. (2008) in Biology of Plant Microbe Interactions Vol. 6, (Matteo L., Ed.), International Society for Molecular Plant-Microbe Interactions, St. Paul, Minnesota, in press.
22. Margulies, M.; Egholm, M.; Altman, W.E.; Attiya, S.; Bader, J.S.; Bemben, L.A.; Berka, J.; Braverman, M..S.; Chen, Y.J.; Chen, Z.; Dewell, S.B.; Du, L.; Fierro, J.M.; Gmes, X.V.; Godwin, B.C.; He, W.; Helgesen, S.; Ho, C.H..; Irzyk, G.P. Jandom S,C.; Alenquer, M.L.; Jarvie, T.P.; Jirage, K.B.; Kim, J.B.; Knight,R.; Lanza, J.R.; Leamon, J.H.; Lefkowitz, S.M.; Lei, M., Li, J.; Lohman, K.L.; Lu, H.; Makhijani, V.B.; McDade, K.E.; McKenna, M.P.; Myers, E.W.; Nickerson, E.; Nobile, J.R.; Plant, R.; Puc, B.P.; Ronan, M.T.; Roth, G.T.; Sarkis, G.J.; Simons, J.F.; Simpson, J.W.; Srinivasan, M.; Tartaro, K.R.; Tomasz, A.; Vogt, K.A.; Volkmer, G.A.; Wang, S.H.; Wang, Y.; Weiner, M.P.; Yu, P.; Begley, R.F. and Rothberg, J.M. (2005) Nature, 437, 376-380.
23. Goldberg, S.M.; Johnson, J.; Busam, D.; Feldblyum, T.; Ferriera, S.; Friedman, R.; Halpern, A.; Khouri, H.; Kravitz, S.A.; Lauro, F.M.; Li, K.; Rogers, Y.H.; Strausberg, R.; Sutton, G..; Tallon, L.; Thomas, T.; Venter, E.; Frazier, M. and Venter, J.C. (2006) Proc. Natl. Acad. Sci. USA, 103, 11240-5.
24. Hafner, M.; Landgraf, P.; Ludwig, J.; Rice, A.; Ojo, T.; Lin, C.; Holoch, D.; Lim, C. and Tuschl, T. (2008) Methods, 44, 3-12
25. Torres, T. T.; Metta, M.; Ottenwälder, B. and Schlötterer, C. (2008) Genome Res., 18,172-7.
26. Cox-Foster, D.L.; Conlan, S.; Holmes, E.C.; Palacios, G..; Evans, J.D.; Moran, N.A.; Quan, P.L.; Briese, T.; Hornig, M.; Geiser, D.M.; Martinson, V.; vanEngelsdorp, D.; Kalkstein, A.L.; Drysdale, A.; Hui, J.; Zhai, J.; Cui, L.; Hutchison, S.K.; Simons, J.F.; Egholm, M.; Pettis, J.S. and Lipkin, W.I. (2007) Science, 318, 283-7.