Yong-Soo Park1, Songmi Kim2,3, Dong-Guk Park4, Dong Hee Kim5, Kyeong-Wook Yoon6, Wonseok Shin7,8, Kyudong Han9,10. 1. Department of Equine Industry, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea. 2. Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea. 3. Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. 4. Department of Surgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea. 5. Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea. 6. Department of Neurosurgery, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea. 7. Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea. w.shin86@gmail.com. 8. Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. w.shin86@gmail.com. 9. Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea. kyudong.han@gmail.com. 10. Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. kyudong.han@gmail.com.
Abstract
BACKGROUND: 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. OBJECTIVE: 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. METHODS: 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. RESULTS: 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. CONCLUSION: The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
BACKGROUND: 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. OBJECTIVE: 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. METHODS: 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. RESULTS: 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. CONCLUSION: The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
Keywords:
Library prep kit; Poly A selection; RNA-Seq; Transcriptome sequencing
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