Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq

ABSTRACT: Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq

PROVIDER: PRJNA749175 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15222627.fastq.gz	Fastqsanger.gz
	SRR15222628.fastq.gz	Fastqsanger.gz
	SRR15222629.fastq.gz	Fastqsanger.gz
	SRR15222630.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Transcriptome-wide identification of RNA binding protein binding sites using seCLIP-seq

Project description:Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP:RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency, and scalability.

2022-02-07 | GSE180686 | GEO

Identification of RRP1 binding sites using seCLIP-seq in IL-1β stimulated RAW 264.7 cells.

Project description:How RRP1 control RNA processing and regulation in macrophage inflammation is important. Here is the identification for RRP1 binding sites by using the single-end enhanced CLIP(seCLIP) in RAW 264.7 cells.

2025-07-02 | GSE292070 | GEO

Identification of RRP1 binding sites using seCLIP-seq in IL-1β stimulated RAW 264.7 cells.

Project description:Identification of RRP1 binding sites using seCLIP-seq in IL-1β stimulated RAW 264.7 cells.

| PRJNA1236643 | ENA

Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

Project description:To check the subcellular location-specific HNRNPK binding sites on mouse SINEB2 repeat element, we prepared seCLIP (single-end enhanced crosslinking and immunoprecipitation assay) libraries from SINEUP-GFP transfected nuclear and cytoplasmic fractions from HEK293T/17 cells.

2023-03-16 | GSE227250 | GEO

Genome-wide identification of protein binding sites in mammalian cells.

Project description:Genome-wide identification of protein binding sites in mammalian cells.

| PRJNA480206 | ENA

Genome-wide identification of protein binding sites in mammalian cells.

Project description:We report the application of genome-wide protein binding sites capture (GWPBS-Cap) technology for high-throughput profiling of protein binding sites in mammalian cells. By obtaining over 37 billion bases of sequence from NaCl washed chromatin DNA in each group, we got an unprecedented view into genome-wide binding patterns of many DNA binding proteins of Hela cells. We find that active promoters contain more PBSs with lower NaCl tolerance and our technology provides a genome-wide landscape of DNA-protein interactions.

2018-07-10 | GSE116770 | GEO

Identification of Transcription Factor Binding Sites using ATAC-seq

Project description:Identification of Transcription Factor Binding Sites using ATAC-seq

| PRJNA484892 | ENA

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

Project description:This SuperSeries is composed of the following subset Series: GSE33569: In vivo and transcriptome-wide identification of RNA-binding protein target sites [PAR-CLIP] GSE33573: In vivo and transcriptome-wide identification of RNA-binding protein target sites [RNA-Seq] Refer to individual Series

2011-12-09 | E-GEOD-33543 | biostudies-arrayexpress

Transcriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq

Project description:iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.

2015-03-09 | E-MTAB-2279 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the following subset Series: GSE21574: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: QKI data GSE21575: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: IGF2BP data GSE21577: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: miRNA inhibition data GSE21918: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data Refer to individual Series

2010-04-29 | E-GEOD-21578 | biostudies-arrayexpress

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