SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing (Q34579795)

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English	SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing	scientific article

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scholarly article

1 reference

Europe PubMed Central

3 August 2017

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing (English)

1 reference

Europe PubMed Central

3 August 2017

author name string

David Loughrey

1

1 reference

Europe PubMed Central

3 August 2017

Kyle E Watters

2

1 reference

Europe PubMed Central

3 August 2017

Alexander H Settle

3

1 reference

Europe PubMed Central

3 August 2017

Julius B Lucks

4

1 reference

Europe PubMed Central

3 August 2017

language of work or name

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publication date

10 October 2014

1 reference

Europe PubMed Central

3 August 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

3 August 2017

42

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Europe PubMed Central

3 August 2017

21

1 reference

Europe PubMed Central

3 August 2017

copyright license

Creative Commons Attribution 4.0 International

3 May 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

describes a project that uses

massive parallel sequencing

1 reference

based on heuristic

inferred from title

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Landscape and variation of RNA secondary structure across the human transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

The cellular environment stabilizes adenine riboswitch RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

The centrality of RNA for engineering gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

SHAPE-Seq: High-Throughput RNA Structure Analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

An RNA Mapping DataBase for curating RNA structure mapping experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

RNA structure prediction: an overview of methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Understanding the transcriptome through RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Understanding the errors of SHAPE-directed RNA structure modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Modeling and automation of sequencing-based characterization of RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Genome-wide measurement of RNA secondary structure in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

SHAPE-directed RNA secondary structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Advances in RNA structure analysis by chemical probing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

RNAstructure: software for RNA secondary structure prediction and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

The centrality of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Accurate SHAPE-directed RNA structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

The Microprocessor complex mediates the genesis of microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

MicroRNAs: genomics, biogenesis, mechanism, and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

7 July 2018

Determination of in vivo RNA structure in low-abundance transcripts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

RNA SHAPE analysis in living cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

HiTRACE: high-throughput robust analysis for capillary electrophoresis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245970

27 October 2018

Cis-acting ribozymes for the production of RNA in vitro transcripts with defined 5' and 3' ends

1 reference

https://pubmed.ncbi.nlm.nih.gov/25303992

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKU909

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

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