Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review

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Author(s)

  • PuiYan Yeung
  • Eugene Yui-Ching Chow
  • HuiQi Hong
  • Leilei Chen
  • Ting-Fung Chan

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Detail(s)

Original languageEnglish
Number of pages12
Journal / PublicationScientific Reports
Volume9
Early online date30 May 2019
Publication statusPublished - 2019

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Abstract

cDNA library preparation is important for many high-throughput sequencing applications, such as RNA G-quadruplex structure sequencing (rG4-seq). A systematic evaluation of the procedures of the experimental pipeline, however, is lacking. Herein, we perform a comprehensive assessment of the 5 key experimental steps involved in the cDNA library preparation of rG4-seq, and identify better reaction conditions and/or enzymes to carry out each of these key steps. Notably, we apply the improved methods to fragmented cellular RNA, and show reduced RNA input requirement, lower transcript abundance variations between biological replicates, as well as lower transcript coverage bias when compared to prior arts. In addition, the time to perform these steps is substantially reduced to hours. Our method and results can be directly applied in protocols that require cDNA library preparation, and provide insights to the further development of simple and efficient cDNA library preparation for different biological applications.

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