Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Circular RNAs are a large class of animal RNAs with regulatory potency (PAR-CLIP)

PROVIDER: PRJNA186746 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR650318.fastq.gz	Fastqsanger.gz
	SRR650319.fastq.gz	Fastqsanger.gz
	SRR650320.fastq.gz	Fastqsanger.gz
	SRR650321.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Homo sapiens

Project description:Circular RNAs are a large class of animal RNAs with regulatory potency (RNA-Seq)

| PRJNA186745 | ENA

Project description:Circular RNAs are a large class of animal RNAs with regulatory potency

| PRJNA187167 | ENA

Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

2022-10-18 | MSV000090547 | MassIVE

Optimized Infra-red photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells

Project description:We report the PAR-CLIP data for endogenous IGF2BP3 protein in colorectal carcinoma cell line (HCT116). In this study, we established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes and compared RNase cleavage conditions. The PAR-CLIP protocol was modified to use single adapter circular ligation approach to increase the efficiency in library preparation and reduce sequence bias. Moreover, we implemented the use of highly-sensitive infra-red (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method “IR-PAR-CLIP”.

2023-08-17 | GSE229653 | GEO

RAD51AP1 associated with RNA in HEK293T cells

Project description:RNAs have versatile roles in DNA damage repair. We here report RAD51AP1 associated with RNAs by PAR-CLIP.

2024-03-11 | GSE252475 | GEO

In vivo and transcriptome-wide identification of RNA-binding protein target sites [RNA-Seq]

Project description:Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish iPAR-CLIP (in vivo PAR-CLIP) to determine, at nucleotide resolution, transcriptome-wide target sites of GLD-1, a conserved, germline-specific translational repressor in C. elegans. We identified 439 reproducible targets and demonstrate an excellent dynamic range of target detection by iPAR-CLIP. Upon GLD-1 knock-down, protein but not mRNA expression of the 439 targets was specifically and highly significantly upregulated, demonstrating functionality. Finally, we discovered strongly conserved GLD-1 binding sites nearby the start codon of target genes. We propose that GLD-1 interacts with the translation machinery nearby the start codon, a so far unknown mode of gene regulation in eukaryotes.

2011-12-09 | GSE33573 | GEO

In vivo and transcriptome-wide identification of RNA-binding protein target sites [PAR-CLIP]

2011-12-09 | GSE33569 | GEO

Homo sapiens

Project description:Homo sapiens PAR-CLIP

| PRJNA230871 | ENA

PAR-CLIP analysis of YB-1 RNA binding in HEK293T cells

Project description:In this study, we performed PAR-CLIP experiment in HEK293T to explore RNAs directly bound by YB-1.

2024-01-18 | GSE249896 | GEO

Mutant FUS and ELAVL4 (HuD) aberrant crosstalk in Amyotrophic Lateral Sclerosis

Project description:Determination of RNAs bound by wildtype and P525L mutant FUS in human iPSC-derived motoneurons using PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation)

2019-06-13 | GSE118347 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data