Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA153959PRJNA140581PRJNA153961

ORGANISM(S): Homo sapiens

PROVIDER: GSE28865 | GEO | 2011/05/15

SECONDARY ACCESSION(S): PRJNA140581

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)

Project description:Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions. We performed duplicate experiments for each variant of the CLIP protocol (CLIP, PAR-CLIP), each protein (HuR, Ago2), and enzymatic digestion (complete T1 digestion, mild MNase digestion). In addition, we performed a single PAR-CLIP experiment with mild T1 digestion.

2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)

2011-05-15 | GSE28859 | GEO

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (mRNA-seq)

Project description:Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions. We performed duplicate mRNA-Seq experiments for cells grown in the presence of modified nucleotides or in normal medium, and following crosslinking at 365nm, 254nm or without crosslinking. In addition, we performed single mRNA-Seq experiments of cells transfected with anti-GFP or anti-HuR siRNA.

2011-05-15 | E-GEOD-28864 | biostudies-arrayexpress

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (mRNA-seq)

2011-05-15 | GSE28864 | GEO

Transcriptome-wide discovery of microRNA binding sites in human brain by Ago2 HITS-CLIP

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-03 | E-GEOD-52084 | biostudies-arrayexpress

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-28 | E-GEOD-77634 | biostudies-arrayexpress

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-04-29 | GSE21578 | GEO