Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts

BioTechniques

Volumn 35, Issue 3, 2003, Pages 510-518

  Hirozane Kishikawa, Tomoko ^a,b   Shiraki, Toshiyuki ^a,b   Waki, Kazunori ^a,b   Nakamura, Mari ^a,b   Arakawa, Takahiro ^a   Kawai, Jun ^a,b   Fagiolini, Michela ^c   Hensch, Takao K ^c   Hayashizaki, Yoshihide ^a,b   Carninci, Piero ^a,b  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b RIKEN   (Japan)

^c RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CLONING; GENES; RNA; TISSUE;

PLASMID LIBRARIES;

DNA;

COMPLEMENTARY DNA; GENE PRODUCT;

ARTICLE; DNA DETERMINATION; DNA LIBRARY; DNA TRANSCRIPTION; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC VARIABILITY; MOLECULAR CLONING; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; QUANTITATIVE ANALYSIS; UNINDEXED SEQUENCE; VALIDATION PROCESS;

EID: 10744226597     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03353st04     Document Type: Article

References (16)

1. Carninci, P., K. Waki, T. Shiraki, H. Konno, K. Shibata, M. Ito, K. Aizawa, T. Arakawa, et al. 2003. Targeting a complex transcriptome: the contruction of the mouse full-length CDNA encyclopedia. Genome Res. 13:1273-1289.
2. Okazaki, Y., M. Furuno, T. Kasukawa, J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563-573.
3. Carninci, P. and Y. Hayashizaki. 1999. High-efficiency full-length cDNA cloning. Methods Enzymol. 303:19-44.
4. Carninci, P., Y. Shibata, N. Hayatsu, Y. Sugahara, K. Shibata, M. Itoh, H. Konno, Y. Okazaki, et al. 2000. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10:1617-1630.
5. Bonaldo, M.F., G. Lennon, and M.B. Soares. 1996. Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 6:791-806.
6. Carninci, P., Y. Shibata, N. Hayatsu, M. Itoh, T. Shiraki, T. Hirozane, A. Watahiki, K. Shibata, et al. 2001. Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel λ-FLC family allows enhanced gene discovery rate and functional analysis. Genomics 77:79-90.
7. Shibata, Y., P. Carninci, A. Watahiki, T. Shiraki, H. Konno, M. Muramatsu, and Y. Hayashizaki. 2001. Cloning full-length, captrapper-selected cDNAs by using the single-strand linker ligation method. BioTechniques 30:1250-1254.
8. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. CSH Laboratory Press, Cold Spring Harbor, NY.
9. Manfioletti, G. and C. Schneider. 1988. A new and fast method for preparing high quality λ DNA suitable for sequencing. Nucleic Acid Res. 16:2873-2884.
10. Boom, R., C.J. Sol, M.M. Salimans, C.L. Jansen, P.M. Wertheim-van Dillen, and J. van der Noordaa. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:495-503.
11. Anderson, M. and B.D. Young. 1985. Quantitative analysis of solution hybridization, p. 73-111. In Nucleic Acids Hybridization, A Practical Approach, IRL Press, Oxford.
12. Konno, H., Y. Fukunishi, K. Shibata, M. Itoh, P. Carninci, Y. Sugahara, and Y. Hayashizaki. 2001. Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library. Genome Res. 11:281-289.
13. Shibata, K., M. Itoh, S. Aizawa, S. Nagaoka, N. Sasaki, P. Carninci, H. Konno, J. Akiyama, et al. 2000. RIKEN integrated sequence analysis (RISA) system-384-format sequencing pipeline with 384 multicapillary sequencer. Genome Res. 10:1757-1771.
14. Sugahara, Y., P. Carninci, M. Itoh, K. Shibata, H. Konno, T. Endo, M. Muramatsu, and Y. Hayashizaki. 2001. Comparative evaluation of 5′-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries. Gene 263:93-102.
15. Press, W.H., B.P. Flannery, S.A. Teukolsky, and W.T. Vetterling. 1988. Numerical Recipes in C. Cambridge University Press, Cambridge, UK.
16. Marra, M., L. Hillier, T. Kucaba, M. Allen, R. Barstead, C. Beck, A. Blistain, M. Bonaldo, et al. 1999. An encyclopedia of mouse genes. Nat. Genet. 21:191-194.