Protocol for using TRIBE to study RNA-protein interactions and nuclear organization in mammalian cells.
Protocol for using TRIBE to study RNA-protein interactions and nuclear organization in mammalian cells.
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DOI：
10.1016/j.xpro.2021.100634
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发表时间：
2021-09-17
期刊：
影响因子：
--
通讯作者：
Rahman R
中科院分区：
文献类型：
--
作者：
Biswas J;Rosbash M;Singer RH;Rahman R
通过编辑发现的RNA结合蛋白的靶标（TRIBE）以最小的假阳性确定RNA-蛋白质相互作用和核组织。我们详细说明了进行哺乳动物细胞RBP-TRIBE以确定RNA结合蛋白的靶点和MS 2-TRIBE以确定细胞核内RNA-RNA相互作用的必要步骤。详细介绍了进行TRIBE实验的必要步骤，从质粒/细胞系生成，细胞转染和RNA测序文库制备开始，并以RNA编辑位点的生物信息学分析和靶RNA的鉴定结束。有关本方案使用和执行的完整详细信息，请参阅。TRIBE和HyperTRIBE可以很容易地在哺乳动物系统中使用HyperTRIBE具有最小的假阳性和假阴性使用虚拟机通过编辑发现的RNA结合蛋白质的目标（TRIBE）确定RNA-蛋白质相互作用和核组织，使分析管道更容易访问。我们详细介绍了进行哺乳动物细胞RBP-TRIBE以确定RNA结合蛋白的靶点和MS 2-TRIBE以确定细胞核内RNA-RNA相互作用的必要步骤。详细介绍了进行TRIBE实验的必要步骤，从质粒/细胞系生成，细胞转染和RNA测序文库制备开始，并以RNA编辑位点的生物信息学分析和靶RNA的鉴定结束。
Targets of RNA-binding proteins discovered by editing (TRIBE) determines RNA-proteins interactions and nuclear organization with minimal false positives. We detail necessary steps for performing mammalian cell RBP-TRIBE to determine the targets of RNA-binding proteins and MS2-TRIBE to determine RNA-RNA interactions within the nucleus. Necessary steps for performing a TRIBE experiment are detailed, starting with plasmid/cell line generation, cellular transfection, and RNA sequencing library preparation and concluding with bioinformatics analysis of RNA editing sites and identification of target RNAs. For complete details on the use and execution of this protocol, please refer to. TRIBE and HyperTRIBE can be readily used in mammalian systems HyperTRIBE has minimal false positives and false negatives The analysis pipeline has been made more accessible using a virtual machine Targets of RNA-binding proteins discovered by editing (TRIBE) determines RNA-proteins interactions and nuclear organization with minimal false positives. We detail necessary steps for performing mammalian cell RBP-TRIBE to determine the targets of RNA-binding proteins and MS2-TRIBE to determine RNA-RNA interactions within the nucleus. Necessary steps for performing a TRIBE experiment are detailed, starting with plasmid/cell line generation, cellular transfection, and RNA sequencing library preparation and concluding with bioinformatics analysis of RNA editing sites and identification of target RNAs.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Van Nostrand EL;Pratt GA;Shishkin AA;Gelboin-Burkhart C;Fang MY;Sundararaman B;Blue SM;Nguyen TB;Surka C;Elkins K;Stanton R;Rigo F;Guttman M;Yeo GW
通讯作者：
Yeo GW
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
5.8
作者：
Biswas, Jeetayu;Rahman, Reazur;Singer, Robert H.
通讯作者：
Singer, Robert H.