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SHAPE-Seq SHAPE-Seq 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. 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.

19.07.2014 · Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule.

We show that SHAPE-Seq v2.0 is highly reproducible, with reactivity data that can be used as constraints in RNA folding algorithms to predict ...

The goal of SHAPE-Seq is to accurately infer nucleotide-resolution structural information through simultaneous SHAPE probing of a mixture of RNA ...

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, t …

SHAPE-seq – reveals a nucleotide-resolution snapshot of RNA folding ... By the time you reach the end of this sentence, RNA folding will have taken place in your ...

As part of this optimization, we present SHAPE-Seq v2.0, a 'universal' method that can obtain reactivity information for every nucleotide of an RNA without having to use or introduce a specific reverse transcriptase priming site within the RNA.

This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, t …

SHAPE-Seq. Selective 2ê-Hydroxyl Acylation Analyzed by Primer Extension Sequencing. SHAPE-Seq provides structural information about RNA (Lucks et al., 2011) (Watters et al., 2016). 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.

01.12.2012 · 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.

SHAPE-Seq SHAPE-Seq 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.

Dec 01, 2012 · 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.

SHAPE-MaP sequences secondary RNA structures at various levels on a massively parallel scale. The method can be customized to interrogate small RNAs, amplicons, or rare RNA species accurately in a mixture of RNAs. As implied in the name, SHAPE-Map uses the SHAPE-Seq 1M7 reaction to mark RNA ribose 2’-OH groups to identify secondary RNA structures.

The basic SHAPE-Seq protocol. In SHAPE-Seq (6 ...

The SHAPE-Seq protocol consists of several core steps. These include: RNA chemical modification, converting RNA into cDNA with reverse ...

The basic SHAPE-Seq protocol. In SHAPE-Seq (6,7), RNAs are modified with chemical probes, such as 1M7 (24), or any probe that covalently ...

05.07.2011 · The goal of SHAPE-Seq is to accurately infer nucleotide-resolution structural information through simultaneous SHAPE probing of a mixture of RNA species ( Fig. 1 ). To explicitly distinguish the species, each RNA in the experiment is bar-coded with a unique nucleotide sequence near the 3′ end of the RNA ( Fig. S1 ).

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 ...

The use of next-generation sequencing allows for higher throughput, more consistent data analysis, and multiplexing capabilities. The technique described herein, SHAPE-Seq v2.0, uses a universal reverse transcription priming site that is ligated to the RNA after SHAPE modification.

Introduction

SHAPE-Seq - Enseqlopedia SHAPE-Seq Selective 2ê-Hydroxyl Acylation Analyzed by Primer Extension Sequencing SHAPE-Seq provides structural information about RNA (Lucks et al., 2011) (Watters et al., 2016). 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.

Mar 30, 2021 · Spats processes reads and calculates SHAPE reactivities for SHAPE-Seq experiments on multiple RNAs. It accepts raw paired-end sequencing reads in fastq format, and a target sequence file containing the sequences of RNAs present in the experimental pool.