Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (eCLIP)

ABSTRACT: Large-scale tethered function assays identify factors that regulate mRNA stability and translation (eCLIP)

PROVIDER: PRJNA482135 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (eCLIP)

Project description:Enhanced UV crosslinking and immunoprecipitation (eCLIP) identifies thousands of endogenous mRNA targets for these prioritized RBPs that respond to protein level changes reminiscent of their effects in tethered functional assay.

2020-08-18 | GSE117290 | GEO

Large-scale tethered function assays identify factors that regulate mRNA stability and translation

Project description:Large-scale tethered function assays identify factors that regulate mRNA stability and translation

| PRJNA482133 | ENA

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (HEK293T_RNA-seq)

Project description:Large-scale tethered function assays identify factors that regulate mRNA stability and translation (HEK293T_RNA-seq)

| PRJNA482136 | ENA

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (polysome profiling)

Project description:Large-scale tethered function assays identify factors that regulate mRNA stability and translation (polysome profiling)

| PRJNA482134 | ENA

Large-scale tethered function assays identify factors that regulate mRNA stability and translation

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

2020-08-18 | GSE117294 | GEO

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.

Project description: Not available

| S-EPMC8221285 | biostudies-literature

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (HEK293T_RNA-seq)

Project description:we either depleted RBPs by lentiviral transduction of short-hairpin RNAs (shRNAs) or ectopically expressed the open reading frame of the protein. For each RBP, we performed two independent transductions of two different targeting shRNAs and two independent transductions of a non-targeting shRNA, or performed two independent transfections with a plasmid directing expression of the RBP as a V5-tagged fusion, with the FLAG construct as a control.

2020-08-18 | GSE117293 | GEO

Large-scale tethered function assays identify factors that regulate mRNA stability and translation (polysome profiling)

Project description:Performed polysome profiling in cell lysates from two independent UBAP2L knockout clonal isolates and from two control samples.

2020-08-18 | GSE117291 | GEO

RBM33 eCLIP

Project description:RBM33 eCLIP

| PRJNA791310 | ENA

Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]

Project description:RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we evaluated 718 human RBPs with tethered function luciferase-based splicing reporter assays to identify 58 candidates, including known splicing factors such as RBFOX and serine-arginine proteins. We performed enhanced CLIP, RNA-seq, and affinity purification-mass spectrometry to investigate a subset of the 11 candidates with no prior association with splicing. Integrative analysis of these assays indicated the surprising roles of TRNAU1AP, SCAF8, and RTCA in modulating hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using identified domains, we engineered programmable fusion proteins which outperformed current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. Altogether, our tethering approach characterized the ability of RBPs to induce exon inclusion and yielded new molecular parts for programmable splicing control.

2023-09-25 | GSE232597 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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