Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of pan-UPF1 knockdown on RNA abundance

ABSTRACT: Flp-In T-REx-293 cells transfected with non-targeting control siRNA or UPF1-specific siRNA as indicated and used for total RNA-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE176197 | GEO | 2022/04/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

UPF1 knockdown in differentiating human myoblasts

Project description:Human myoblast cell line 54-1 is transfected with either a srambled control siRNA or siRNA against UPF1. Two days after transfection, cell were induced to differentiate by changing grow meida to differentiation media. 2 days after induction of differentiation, cells are collected for extraction of RNA.

2017-08-31 | GSE87679 | GEO

Effects of pan-UPF1 knockdown on RNA abundance

Project description:Effects of pan-UPF1 knockdown on RNA abundance

| PRJNA735254 | ENA

Condition- and isoform-dependent UPF1 activity

Project description:HEK-293 cells transfected with non-targeting control siRNA or UPF1LL-specific siRNA were treated with vehicle control, puromycin, or thapsigargin as indicated and used for total RNA-seq.

2022-04-07 | GSE162699 | GEO

MOV10 is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation Along 3' UTRs (PAR-CLIP)

Project description:RNA helicases are important regulators of gene expression that act by remodeling RNA secondary structures and as RNA-protein interactions. Here, we demonstrate that MOV10 has an ATP-dependent 5' to 3' in vitro RNA unwinding activity and determine the RNA-binding sites of MOV10 and its helicase mutants using PAR-CLIP. We find that MOV10 predominantly binds to 3' UTRs upstream of regions predicted to form local secondary structures and provide evidence that MOV10 helicase mutants are impaired in their ability to translocate 5' to 3' on their mRNA targets. MOV10 interacts with UPF1, the key component of the nonsense-mediated mRNA decay pathway. PAR-CLIP of UPF1 reveals that MOV10 and UPF1 bind to RNA in close proximity. Knockdown of MOV10 resulted in increased mRNA half-lives of MOV10-bound as well as UPF1-regulated transcripts, suggesting that MOV10 functions in UPF1-mediated mRNA degradation as an RNA clearance factor to resolve structures and displace proteins from 3' UTRs. Flp-In T-REx HEK293 cells expressing FLAG/HA-tagged MOV10 WT, MOV10 K530A, MOV10 D645N and UPF1 were sequenced. mRNA half-life data under GSE56751.

2014-04-11 | E-GEOD-48245 | biostudies-arrayexpress

MOV10 Is a 5' to 3' RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3'UTRs (expression)

2014-04-11 | E-GEOD-56748 | biostudies-arrayexpress

UPF1 regulatory loop variant RNA-Seq and RIP-Seq

Project description:HEK-293 Trex cells containing stable tetracycline-inducible transgenes driving overexpression of CLIP-tagged UPF1 isoforms 1 and 2 or GFP were used for total RNA-seq. In addition, CLIP-UPF1 isoforms were affinity purified, and bound RNA was subjected to high-throughput sequencing.

2020-05-28 | GSE134059 | GEO

Splicing activation by Rbfox requires self-aggregation through its tyrosine-rich domain

Project description:To determine how the higher order assembly of Rbfox proteins affect Rbfox-dependent splicing regulation, we expressed Rbfox wildtype and its mutant protein in Flp-In™ T-REx™ 293 Rbfox2-/- cells and extracted RNA from these cells to perform RASL-seq which profiles thousands of alternative splicing event.

2017-07-13 | GSE89597 | GEO

Searching for interactors of endogenous SLX4

Project description:The project was aimed at identifying binding partners of endogenous SLX4 in HeLa cells. Whole cell extracts from HeLa Flp-In T-Rex cells were used for immunoprecipitation performed with anti-SLX4 antibodies from Bethyl Laboratories (A302-270A and A302-269A), either used alone or in combination. To discriminate bona fide SLX4 partners from non-specific proteins recognized by the anti-SLX4 antibodies, cells were transfected with control (Luc) siRNA or a siRNA targeting SLX4. After immunoprecipitation, protein complexes were analysed by LC-MSMS.

2022-02-16 | PXD029084 | Pride

PTBP1 excludes UPF1 to protect long 3'UTRs from nonsense-mediated mRNA decay

Project description:RNA-seq analysis of human 293 Tet-off cells depleted of PTBP1 and UPF1 alone and in tandem with specific siRNAs.

2016-01-21 | GSE59884 | GEO

RNA-Seq of control and RNPS1 knockdown with or without RNPS1 wildtype or RNPS1-RRM domain rescue in Flp-In T-REx 293 cells

Project description:RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative splicing events. We aimed to investigate in Flp-In T-REx 293 cells which alternative splicing events are rescued by the expression of the wild type RNPS1 or the isolated RRM domain of RNPS1 in a RNPS1 knockdown background by using RNA-Seq analyses. The rescue construct was stably integrated into the genome using the PiggyBac transposon system. As controls, either Luciferase (Luc) siRNA was used or RNPS1 was knocked down without rescue.

2022-05-06 | E-MTAB-10770 | 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