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Detecting Expressed Genes Using CAGE

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Transcription Factor Regulatory Networks

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.

All the authors contributed equally to this work.

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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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Correspondence to Masayoshi Itoh .

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Murata, M., Nishiyori-Sueki, H., Kojima-Ishiyama, M., Carninci, P., Hayashizaki, Y., Itoh, M. (2014). Detecting Expressed Genes Using CAGE. In: Miyamoto-Sato, E., Ohashi, H., Sasaki, H., Nishikawa, Ji., Yanagawa, H. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 1164. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0805-9_7

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  • DOI: https://doi.org/10.1007/978-1-4939-0805-9_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0804-2

  • Online ISBN: 978-1-4939-0805-9

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