CAGE: cap analysis of gene expression

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Figure 1: Preparation of CAGE libraries.


  1. 1

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

  2. 2

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

  3. 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).

  4. 4

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

  5. 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).

  6. 6

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

  7. 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).

  8. 8

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

  9. 9

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

  10. 10

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

  11. 11

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

  12. 12

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

  13. 13

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

  14. 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).

  15. 15

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

  16. 16

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

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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).

Author information

Correspondence to Matthias Harbers or 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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