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CAGE: cap analysis of gene expression

Nature Methods volume 3, pages 211–222 (2006)Cite this article

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Figure 1: Preparation of CAGE libraries.

References

  1. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kinzler, K.W. Serial analysis of gene expression. Science 270, 484–487 (1995).

    Article  CAS  Google Scholar 

  2. Brenner, S. et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630–634 (2000).

    Article  CAS  Google Scholar 

  3. Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 100, 15776–15781 (2003).

    Article  CAS  Google Scholar 

  4. Hashimoto, S. et al. 5′-end SAGE for the analysis of transcriptional start sites. Nat. Biotechnol. 22, 1146–1149 (2004).

    Article  CAS  Google Scholar 

  5. Wei, C.L. et al. 5′ long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl. Acad. Sci. USA 101, 11701–11706 (2004).

    Article  CAS  Google Scholar 

  6. Cheng, J. et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).

    Article  CAS  Google Scholar 

  7. Kodzius, R. et al. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Lett. 559, 22–26 (2004).

    Article  CAS  Google Scholar 

  8. Lagonigro, M.S. et al. CTAB-urea method purifies RNA from melanin for cDNA microarray analysis. Pigment Cell Res. 17, 312–315 (2004).

    Article  CAS  Google Scholar 

  9. Carninci, P. & Hayashizaki, Y. High-efficiency full-length cDNA cloning. Methods Enzymol. 303, 19–44 (1999).

    Article  CAS  Google Scholar 

  10. Carninci, P. et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327–336 (1996).

    Article  CAS  Google Scholar 

  11. Schofield, G.G. PicoGmeter, a custom-made fluorometer for the quantification of dsDNA by PicoGreen fluorescence. Biotechniques 37, 778–780, 782 (2004).

    Article  CAS  Google Scholar 

  12. Jones, M.L. & Kurzban, G.P. Noncooperativity of biotin binding to tetrameric streptavidin. Biochemistry 34, 11750–11756 (1995).

    Article  CAS  Google Scholar 

  13. Ishikawa, T. et al. Use of transcriptional sequencing in difficult to read areas of the genome. Anal. Biochem. 316, 202–207 (2003).

    Article  CAS  Google Scholar 

  14. Shibata, K., Izawa, M., Hayashizaki, Y. & Watahiki, M. Practical application of transcriptional sequencing for GC-rich templates. J. Struct. Funct. Genomics 4, 35–39 (2003).

    Article  CAS  Google Scholar 

  15. Carninci P. et al. The transcription landscape of the mammalian genome. Science 309, 1559–1563 (2005).

    Article  CAS  Google Scholar 

  16. Katayama S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564–1566 (2005).

    Article  Google Scholar 

Download references

Acknowledgements

We are grateful to S. Kondo and A. Hasegawa for help with bioinformatics, and H. Sato, C. Kawazu, S. Kanagawa, M. Ohno, M. Murata, K. Nomura, Y. Tagami-Takeda and K. Hayashida for support in developing, producing and sequencing CAGE libraries. This protocol was developed with the support of the Genome Network Project, the Advanced and Innovational Research Program in Life Science and the Research Grant for RIKEN Genome Exploration Research Project, all from the Ministry of Education, Culture, Sports, Science and Technology, as well as the Strategic Programs for Research and Development of RIKEN. R.K. was supported by a fellowship from the European Union (FP5 INCO2 to Japan).

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Author notes

  1. Rimantas Kodzius

    Present address: Vaxine Pty Ltd., Department of Diabetes and Endocrinology, Flinders Medical Centre, Bedford Park, Southern Australia, 5042, Australia

Authors and Affiliations

  1. Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan

    Rimantas Kodzius, Miki Kojima, Hiromi Nishiyori, Mari Nakamura, Shiro Fukuda, Michihira Tagami, Daisuke Sasaki, Kengo Imamura, Chikatoshi Kai, Yoshihide Hayashizaki & Piero Carninci

  2. Genome Science Laboratory, RIKEN, Wako main campus, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan

    Rimantas Kodzius, Yoshihide Hayashizaki & Piero Carninci

  3. K.K. Dnaform, Tsukuba Branch, 3-1 Chuo 8-chome, Ami Machi, Inashiki Gun, 300-0332, Ibaraki, Japan

    Matthias Harbers

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Corresponding authors

Correspondence to Matthias Harbers, Yoshihide Hayashizaki or Piero Carninci.

Supplementary information

Supplementary Fig. 1

Flowchart for the high-throughput preparation of full-length enriched cDNAs. (PDF 149 kb)

Supplementary Table 1

Oligonucleotides for use in CAGE protocol. (DOC 26 kb)

Supplementary Table 2

CAGE Linker Oligos. (PDF 312 kb)

Supplementary Table 3

HPLC gradient used for fractionation of concatemers. (DOC 563 kb)

Supplementary Methods (DOC 36 kb)

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Kodzius, R., Kojima, M., Nishiyori, H. et al. CAGE: cap analysis of gene expression. Nat Methods 3, 211–222 (2006). https://doi.org/10.1038/nmeth0306-211

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