Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing
Joint Authors
Pan, Cheng-Tsung
Lin, Wei-Chen
Tsai, Kuo-Wang
Li, Sung-Chou
Chang, Bill
Chen, Ting-Wen
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-03-29
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Abstract EN
Next-generation sequencing (NGS) has become a powerful sequencing tool, applied in a wide range of biological studies.
However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS), leading to biased estimates of expression for transcripts overlapped at the antisense strand.
Strand-specific (SS) protocols have recently been developed.
In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform.
Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand.
In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects.
Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located.
Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes.
Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.
American Psychological Association (APA)
Tsai, Kuo-Wang& Chang, Bill& Pan, Cheng-Tsung& Lin, Wei-Chen& Chen, Ting-Wen& Li, Sung-Chou. 2015. Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing. BioMed Research International،Vol. 2015, no. 2015, pp.1-8.
https://search.emarefa.net/detail/BIM-1054525
Modern Language Association (MLA)
Tsai, Kuo-Wang…[et al.]. Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing. BioMed Research International No. 2015 (2015), pp.1-8.
https://search.emarefa.net/detail/BIM-1054525
American Medical Association (AMA)
Tsai, Kuo-Wang& Chang, Bill& Pan, Cheng-Tsung& Lin, Wei-Chen& Chen, Ting-Wen& Li, Sung-Chou. Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-8.
https://search.emarefa.net/detail/BIM-1054525
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1054525