Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HNRNPU MY-CLIP study using cytoplasmic or whole lysates

ABSTRACT: HNRNPU MY-CLIP study using cytoplasmic or whole lysates

PROVIDER: PRJNA576694 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10493725.fastq.gz	Fastqsanger.gz
	SRR10493726.fastq.gz	Fastqsanger.gz
	SRR10493727.fastq.gz	Fastqsanger.gz
	SRR10493728.fastq.gz	Fastqsanger.gz
	SRR10493729.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

HNRNPU MY-CLIP study using cytoplasmic or whole lysates

Project description:Comparison of MY-CLIP between using cytoplasmic fraction and whole cell lysate for PMA/Ca2+ ionophore stimuated HeLa cells

2020-03-31 | GSE138661 | GEO

MY-CLIP verification study

Project description:Comparison between BrdU-CLIP and MY-CLIP for HNRNPU, and MY-CLIP performance for HNRNPC

2020-03-31 | GSE138649 | GEO

Analysis of the translocating RNA-binding protein HNRNPU using MY-CLIP

Project description:Analysis of the translocating RNA-binding protein HNRNPU using MY-CLIP

| PRJNA576904 | ENA

MY-CLIP verification study

Project description:MY-CLIP verification study

| PRJNA576684 | ENA

HITS-CLIP of cytoplasmic SLBP RNP

Project description:UV cross-linking and immunoprecipiatation with high throughput sequencing of cytoplasmic SLBP RNP Polyclonal Î±-SLBP antibody was used to immunoprecipitate UV-crosslinked SLBP RNP from cytoplasmic HeLa lysates. Mock immunoprecipitation were also performed and serve as a negative control.

2015-12-16 | E-GEOD-61958 | biostudies-arrayexpress

Analysis of the translocating RNA-binding protein HNRNPU using MY-CLIP

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

2020-03-31 | GSE138726 | GEO

HNRNPU regulates lncRNAs nuclear localization

Project description:To elucidate the role of HNRNPU in regulation of lncRNAs nuclear localization, we knocked down HNRNPU in K562 cells using short interfering RNAs and performed subcellular RNA-seq using nuclear or cytosolic RNAs

2021-01-23 | GSE165310 | GEO

Gene expression and splicing regulation by hnRNPU in skeletal muscle

Project description:Hnrnpu is the largest member of the heterogenous nuclear ribonucleoprotein family of RNA binding proteins. Hnrnpu is involved in pre-mRNA alternative splicing regulation. We used high throughput sequencing to determine how Hnrnpu regulates skeletal muscle physiology.

2020-07-06 | GSE145712 | GEO

Transcriptomic analysis of gastric cancer cells in response to stable over-expression of circRNA derived from hnRNPU (circ-hnRNPU)

Project description:Circular RNA (circRNA) is a type of endogenous single-stranded and covalently closed non-coding RNA that plays emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating gastric cancer progression still remain elusive. We identify circ-hnRNPU, a circRNA derived from exons 5, 6, 7 and 8 of heterogeneous nuclear ribonucleoprotein U (hnRNPU), as a tumor suppressor of gastric cancer progression. To investigate the mechanisms underlying the functions of circ-hnRNPU, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human gastric cancer MKN-45 and AGS cells in response to stable over-expression of circ-hnRNPU. The results showed that stable over-expression of circ-hnRNPU led to altered expression of 112 human mRNAs, including 64 up-regulated and 48 down-regulated genes, in both MKN-45 and AGS cells. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to circ-hnRNPU over-expression in human gastric cancer cells, and these findings will help us understand the pathogenesis of cancer progression.

2024-11-02 | GSE246847 | GEO

Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs

Project description:We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis. To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).

2013-11-07 | E-GEOD-50989 | 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