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RNA Sequencing of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining
المؤلفون المشاركون
Cai, Qiuyin
Sheng, Quanhu
Lehmann, Brian
Clark, Travis
Wu, Jie
Su, Yinghao
Shu, Xiao-ou
Guo, Yan
Zhao, Shilin
Ye, Fei
المصدر
International Journal of Genomics
العدد
المجلد 2016، العدد 2016 (31 ديسمبر/كانون الأول 2016)، ص ص. 1-10، 10ص.
الناشر
Hindawi Publishing Corporation
تاريخ النشر
2016-09-28
دولة النشر
مصر
عدد الصفحات
10
التخصصات الرئيسية
الملخص 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.
نمط استشهاد جمعية علماء النفس الأمريكية (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
نمط استشهاد الجمعية الأمريكية للغات الحديثة (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
نمط استشهاد الجمعية الطبية الأمريكية (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
نوع البيانات
مقالات
لغة النص
الإنجليزية
الملاحظات
Includes bibliographical references
رقم السجل
BIM-1106194
قاعدة معامل التأثير والاستشهادات المرجعية العربي "ارسيف Arcif"
أضخم قاعدة بيانات عربية للاستشهادات المرجعية للمجلات العلمية المحكمة الصادرة في العالم العربي
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