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SHAPE-Seq: High-Throughput RNA Structure Analysis

Mortimer, Stefanie A. and Trapnell, Cole and Aviran, Sharon and Pachter, Lior and Lucks, Julius B. (2012) SHAPE-Seq: High-Throughput RNA Structure Analysis. In: Current Protocols in Chemical Biology. John Wiley and Sons , New York, NY, pp. 275-297. ISBN 9780470559277.

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Knowledge of RNA structure is critical to understanding both the important functional roles of RNA in biology and the engineering of RNA to control biological systems. 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. This protocol is applicable in a variety of conditions, and represents an important tool for understanding RNA biology. The protocol includes methods for the design and synthesis of RNA mixtures for study, and the construction and analysis of structure-dependent sequencing libraries that reveal structural information of the RNAs in the mixtures. The methods are generally applicable to studying RNA structure and interactions in vitro in a variety of conditions, and allows for the rapid characterization of RNA structures in a high-throughput manner.

Item Type:Book Section
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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2012 John Wiley and Sons.
Subject Keywords:RNA structure; next-generation sequencing; chemical probing; high throughput
Record Number:CaltechAUTHORS:20170303-160835568
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Official Citation:Mortimer, S. A., Trapnell, C., Aviran, S., Pachter, L. and Lucks, J. B. 2012. SHAPE–Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4:275–297.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74742
Deposited By: George Porter
Deposited On:06 Mar 2017 16:30
Last Modified:11 Nov 2021 05:29

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