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Updated: Jul 6, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Degradome Sequencing
Shih-Shun Lin1, Yihua Chen2, Mei-Yeh Jade Lu3
1Institute of Biotechnology, National Taiwan University, Taipei, Taiwan. linss01@ntu.edu.tw.
Abstract:
Degradome sequencing provides comprehensive insights into RNA degradation profiles. The method described here adapts the 5'-rapid amplification of cDNA ends (5'-RACE) technique, enabling the sequencing of degradome cDNA fragments using short-read next-generation sequencing (NGS). Degradome profiles can validate predicted miRNA-mediated cleavage of target genes and identify novel targets. Additionally, this approach offers valuable insights into RNA processing mechanisms, including the roles of RNA-binding proteins. This chapter outlines an optimized protocol for constructing a high-yield, high-quality degradome library, encompassing NGS and data analysis procedures. We anticipate that the degradome sequencing approach will be highly beneficial for studying RNA dynamics in non-model organisms.
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