Chapter title |
High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA
|
---|---|
Chapter number | 13 |
Book title |
miRNA Biogenesis
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8624-8_13 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8623-1, 978-1-4939-8624-8
|
Authors |
Josephine Galipon, Rintaro Ishii, Soh Ishiguro, Yutaka Suzuki, Shinji Kondo, Mariko Okada-Hatakeyama, Masaru Tomita, Kumiko Ui-Tei, Galipon, Josephine, Ishii, Rintaro, Ishiguro, Soh, Suzuki, Yutaka, Kondo, Shinji, Okada-Hatakeyama, Mariko, Tomita, Masaru, Ui-Tei, Kumiko |
Abstract |
Paired-end RNA sequencing (RNA-seq) is usually applied to the quantification of long transcripts such as messenger or long non-coding RNAs, in which case overlapping pairs are discarded. In contrast, RNA-seq on short RNAs (≤ 200 nt) is typically carried out in single-end mode, as the additional cost associated with paired-end would only translate into redundant sequence information. Here, we exploit paired-end sequencing of short RNAs as a strategy to filter out sequencing errors and apply this method to the identification of adenosine-to-inosine (A-to-I) RNA editing events on human precursor microRNA (pre-miRNA) and mature miRNA. Combined with RNA immunoprecipitation sequencing (RIP-seq) of A-to-I RNA editing enzymes, this method takes full advantage of deep sequencing technology to identify RNA editing sites with unprecedented resolution in terms of editing efficiency. |
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Members of the public | 2 | 100% |
Mendeley readers
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Unknown | 13 | 100% |
Demographic breakdown
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Researcher | 3 | 23% |
Student > Master | 2 | 15% |
Student > Bachelor | 1 | 8% |
Professor | 1 | 8% |
Student > Doctoral Student | 1 | 8% |
Other | 3 | 23% |
Unknown | 2 | 15% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 4 | 31% |
Unspecified | 1 | 8% |
Unknown | 4 | 31% |