SHAPE-Seq - Illumina
SHAPE-Seq provides structural information about RNA. In this method, a unique barcode is first added to the 3' end of RNA, and the RNA is allowed to fold under pre-established in vitro conditions. The barcoded and folded RNA is treated with a SHAPE reagent, 1-methyl-7-nitroisatoic anhydride (1M7), which blocks RT.
SHAPE-Seq: High-Throughput RNA Structure Analysis
2012年12月1日 · This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment.
Multiplexed RNA structure characterization with selective 2′ …
2011年6月3日 · We demonstrate the ability of SHAPE-Seq to accurately infer secondary and tertiary structural information, detect subtle conformational changes due to single nucleotide point mutations, and simultaneously measure the structures of a complex pool of …
生命学院薛毅课题组利用SHAPE数据特征提高RNA二级结构预测的 …
近年来，化学小分子探针被广泛应用于RNA二级结构的探测，其中，selective 2´-hydroxyl acylation analyzed by primer extension（SHAPE）技术利用亲电试剂对不同状态碱基（配对或未配对）的修饰活性的差异来实现对RNA二级结构的探测。
SHAPE-Seq 2.0: systematic optimization and extension of high …
2014年10月10日 · Here, we present the first analysis and optimization of these effects for selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). We first optimize SHAPE-Seq, and show that it provides highly reproducible reactivity data over a wide range of RNA structural contexts with no apparent biases.
SHAPE-Seq - Illumina
Selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) provides structural information about RNA. In this method, a unique barcode is first added to the 3’ end of RNA, and the RNA is then allowed to fold under pre-established in vitro conditions.
RNA motif discovery by SHAPE and mutational profiling (SHAPE …
2014年7月13日 · Sites of 2′-hydroxyl acylation by SHAPE are encoded as noncomplementary nucleotides during cDNA synthesis, as measured by massively parallel sequencing. SHAPE-MaP–guided modeling identified...
Transcriptome-wide interrogation of RNA secondary structure …
2016年1月14日 · In SHAPE-seq 16, a pool of in vitro –transcribed RNAs are subjected to SHAPE chemical probing and deep sequencing. This approach has revealed structural changes that occur because of primary...
In-cell RNA structure probing with SHAPE-MaP - Nature Protocols
2018年5月3日 · We detail several strategies by which in-cell SHAPE-MaP can inform new biological hypotheses and emphasize downstream analyses that reveal sequence or structure motifs important for RNA ...
SHAPE–Seq: High-Throughput RNA Structure Analysis - Current …
2012年12月1日 · This article contains a protocol for selective 2′-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment.
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