Detecting Expressed Genes Using CAGE

  • Mitsuyoshi Murata
  • Hiromi Nishiyori-Sueki
  • Miki Kojima-Ishiyama
  • Piero Carninci
  • Yoshihide Hayashizaki
  • Masayoshi Itoh
Part of the Methods in Molecular Biology book series (MIMB, volume 1164)

Abstract

Cap analysis of gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. By the large-scale analysis of 5′ end of transcripts using CAGE method, it enables not only determination of the transcription start site but also prediction of promoter region. Here we provide a protocol for the construction of no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE). We have excluded the commonly used PCR amplification and cleavage of restriction enzyme to eliminate any potential biases. As a result, we achieved less biased simple preparation process.

Key words

Cap analysis of gene expression (CAGE) RNA expression Transcription start site (TSS) Promoter Next-generation sequencing (NGS) 

Notes

Acknowledgement

This work was funded by a Research Grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology through the Cell Innovation Project and for the RIKEN Omics Science Center to Y.H.

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Mitsuyoshi Murata
    • 1
  • Hiromi Nishiyori-Sueki
    • 1
  • Miki Kojima-Ishiyama
    • 1
  • Piero Carninci
    • 1
  • Yoshihide Hayashizaki
    • 2
  • Masayoshi Itoh
    • 2
  1. 1.Division of Genomic Technologies, RIKEN Center for Life Science TechnologiesRIKEN Yokohama InstituteTsurumi-ku, YokohamaJapan
  2. 2.RIKEN Preventive Medicine and Diagnosis Innovation ProgramRIKEN Wako InstituteWakoJapan

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