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.
Highlights
CDNA library preparation is important for many high-throughput sequencing applications, such as RNA G-quadruplex structure sequencing
The new libraries were found to have lower transcript abundance variations and lower 5′ and 3′ transcript coverage bias when compared to prior arts[9]
RSAP reached to completion at 15 minutes (Fig. 2B, lane 5), whereas that of Fast AP happened at around 15 to 30 minutes time (Fig. 2C, lane 5 and 6)
Summary
CDNA library preparation is important for many high-throughput sequencing applications, such as RNA G-quadruplex structure sequencing (rG4-seq). To carry out both enzymatic digestion and column purification steps, after the incubation, 28 μl of nuclease-free water was added to the reaction mixture to dilute the PEG concentration, and purified with
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