Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

ABSTRACT: Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

PROVIDER: PRJNA564016 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10071151.fastq.gz	Fastqsanger.gz
	SRR10071152.fastq.gz	Fastqsanger.gz
	SRR10071153.fastq.gz	Fastqsanger.gz
	SRR10071154.fastq.gz	Fastqsanger.gz
	SRR10071155.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

Project description:To better understand the mechanism of U1A functions in human cells, we performed U1A iCLIP-seq analysis in HeLa cells. iCLIP-seq is a previously well-established protocol that is believed to detect protein-RNA interaction at individual-nucleotide resolution. Indeed, successful completion of U1A iCLIP-seq has helped us to illuminate more detailed mechanism through which U1 snRNP prevents mRNA PCPA (premature cleavage and polyadenylation)

2020-02-28 | GSE146018 | GEO

U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

Project description:U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

| PRJNA609061 | ENA

Identification of Meiotic-P26-bound RNAs in cutlured Drosophila SL2 cells by iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation)

Project description:Identification of Meiotic-P26-bound RNAs in cutlured Drosophila SL2 cells by iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation)

| PRJNA638097 | ENA

Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

Project description:Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

| PRJNA556264 | ENA

Individual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments.

2014-02-13 | GSE37560 | GEO

Individual-nucleotide resolution CLIP and high-throughput sequencing for FOX2, TDP43 and hnRNP M in WT and P-KO H9 cells

2016-10-13 | GSE85851 | GEO

Individual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells

2014-02-13 | E-GEOD-37560 | biostudies-arrayexpress

Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Project description:Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen) Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq. Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA. Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

2019-09-06 | GSE136907 | GEO

iCLIP and NGS to map protein-RNA interactions for U1-snRNP proteins in Trypanosoma brucei

Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei.

2014-05-16 | GSE43848 | GEO

Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)

Project description:To investigate whether the ALKBH5-mediated metabolic changes via demethylation of its target mRNA(s) is important in regulating viral response, we mapped the targeting transcripts and binding sites of ALKBH5 in the virus infected cells and uninfected cells by using iCLIP-seq. Biological replicates of iCLIP-seq confirmed that OGDH is the direct targeting transcript of ALKBH5 and the binding capacity of ALKBH5 to OGDH mRNA was decreased upon viral infection. By combining the ALKBH5-iCLIP-seq results with m6A-seq data, we identified that there are overlapped ALKBH5-iCLIP peaks and m6A-seq peaks on OGDH mRNA. Furthermore, other mRNAs, such as GOT2 mRNA, were also the ALKBH5’s targeting transcripts and m6A demethylation substrates. GOT2 is an important metabolic enzyme well known to be involved in host response to viral infection. These data demonstrated that ALKBH5-mediated metabolic rewiring via demethylation of target OGDH mRNA and other transcripts is important in regulating cellular viral replication.

2019-08-22 | GSE134754 | 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