RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining
Joint Authors
Cai, Qiuyin
Sheng, Quanhu
Lehmann, Brian
Clark, Travis
Wu, Jie
Su, Yinghao
Shu, Xiao-ou
Guo, Yan
Zhao, Shilin
Ye, Fei
Source
International Journal of Genomics
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-09-28
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Background.
Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression.
We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H.
RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced ( N = 16 ).
We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens.
Results.
Both rRNA depletion methods produced consistent data between the technical replicates.
We found that the RNase H method produced higher quality RNAseq data as compared to the Ribo-Zero method.
In addition, we evaluated the RNAseq data generated from the FFPE tissue samples for noncoding RNA, including lncRNA, enhancer/super enhancer RNA, and single nucleotide variation (SNV).
We found that the RNase H is more suitable for detecting high-quality, noncoding RNAs as compared to the Ribo-Zero and provided more consistent molecular subtype identification between replicates.
Unfortunately, neither method produced reliable SNV data.
Conclusions.
In conclusion, for FFPE specimens, the RNase H rRNA depletion method performed better than the Ribo-Zero.
Neither method generates data sufficient for SNV detection.
American Psychological Association (APA)
Guo, Yan& Wu, Jie& Zhao, Shilin& Ye, Fei& Su, Yinghao& Clark, Travis…[et al.]. 2016. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining. International Journal of Genomics،Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1106194
Modern Language Association (MLA)
Guo, Yan…[et al.]. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining. International Journal of Genomics No. 2016 (2016), pp.1-10.
https://search.emarefa.net/detail/BIM-1106194
American Medical Association (AMA)
Guo, Yan& Wu, Jie& Zhao, Shilin& Ye, Fei& Su, Yinghao& Clark, Travis…[et al.]. RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining. International Journal of Genomics. 2016. Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1106194
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1106194