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Duplicate Ditag Analysis in LongSAGE

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Serial Analysis of Gene Expression (SAGE)

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 387))

Summary

The Long serial analysis of gene expression (SAGE) protocol generates ditags from tags with overlapping overhangs, thereby increasing the probability of duplicate ditag formation in LongSAGE. In this chapter, a tool is presented that facilitates the analysis of duplicate ditags in LongSAGE studies to determine whether they should be included or not.

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Reference

  1. Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 270(5235), 484–487.

    Google Scholar 

  2. Saha, S., Sparks, A. B., Rago, C., et al. (2002) Using the transcriptome to annotate the genome. Nat Biotechnol. 20(5), 508–512.

    Google Scholar 

  3. Heidenblut, A. M., Luttges, J., Buchholz, M., et al. (2004) aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells. Nucleic Acids Res. 32(16), e131.

    Google Scholar 

  4. Vilain, C., Libert, F., Venet, D., Costagliola, S., and Vassart, G. (2003) Small amplified RNA-SAGE: an alternative approach to study transcriptome from limiting amount of mRNA. Nucleic Acids Res. 31(6), e24.

    Google Scholar 

  5. Dinel, S., Bolduc, C., Belleau, P., et al. (2005) Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome. Nucleic Acids Res. 33(3), e26.

    Google Scholar 

  6. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998. 8(3), 186–194.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biochemistry, Chemistry, and Environmental Engineering, University of Aalborg, Aalborg, Denmark

    Jeppe Emmersen

Authors
  1. Jeppe Emmersen
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Editor information

Editors and Affiliations

  1. Department of Life Sciences, Aalborg University, Aalborg, Denmark

    KĂĄre Lehmann Nielsen

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Emmersen, J. (2008). Duplicate Ditag Analysis in LongSAGE. In: Nielsen, K.L. (eds) Serial Analysis of Gene Expression (SAGE). Methods in Molecular Biology™, vol 387. Humana Press. https://doi.org/10.1007/978-1-59745-454-4_11

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  • DOI: https://doi.org/10.1007/978-1-59745-454-4_11

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-676-4

  • Online ISBN: 978-1-59745-454-4

  • eBook Packages: Springer Protocols

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