Comparison of library construction kits for mRNA sequencing in the Illumina platform



The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis.


Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction.


We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq® RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output.


The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments.


The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.

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This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science & ICT (2016M3A9B6026776).

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Correspondence to Wonseok Shin or Kyudong Han.

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Yong-Soo Park, Songmi Kim, Dong-Guk Park, Dong Hee Kim, Kyeong-Wook Yoon, Wonseok Shin and Kyudong Han declare that we have no conflict of interest.

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Park, YS., Kim, S., Park, DG. et al. Comparison of library construction kits for mRNA sequencing in the Illumina platform. Genes Genom 41, 1233–1240 (2019).

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  • Transcriptome sequencing
  • RNA-Seq
  • Library prep kit
  • Poly A selection