Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide mapping of MARF1-bound mRNAs

ABSTRACT: To comprehensively identify MARF1-associated mRNAs, we performed iCLIP using engineered HEK293 cells stably expressing a doxycycline (Dox)-inducible FLAG-tagged MARF1 that lacks RNAse activity. Our iCLIP analysis of MARF1 in HEK293 cells identified 108 mRNAs bound by MARF1 and demonstrates that MARF1 binds to the majority of these mRNAs via their 3’UTRs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149820 | GEO | 2020/06/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome-wide mapping of MARF1-bound mRNAs

Project description:Transcriptome-wide mapping of MARF1-bound mRNAs

| PRJNA630233 | ENA

Comparing the Transcriptomes of Marf1-genetrap (GT) oocytes with those microinjected with mRNAs for wild type MARF1 (GTWT) or D272-mutated MARF1 (GTD272) by RNA-Seq Analysis

Project description:The goal of this study is to reveal the globle effect of supplementation with either wild type MARF1or D272-mutated MARF1 on the steady-state levels of mRNAs in Marf1-gene trap GV-stage fully-grown oocytes(FGOs) by comparing the corresponding transcriptomes via RNA-Seq Analysis.

2018-11-14 | GSE109195 | GEO

Functional Significance of U2AF1 S34F Mutation in Lung Adenocarcinomas

Project description:We conducted RNA-Seq and iCLIP for dox-inducible constructs of FLAG-HA tagged U2AF1 in the wild-type and mutant forms.

2019-10-25 | GSE123989 | GEO

MARF1_APMS_Nishimura_V2

Project description:This set of submissions contains the mass spectrometry files for the manuscript by Tamiko Nishimura et al. that describes characterization of MARF1, titled "MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs". Affinity purification of MARF1 is performed in biological duplicates using lysates of Flp-In T-REx HEK293 cells stably expressing FLAG tagged MARF1 and compared to 6 negative controls using SAINTexpress. MS files were acquired on AB SCIEX Triple TOF 6600 instrument. See README file and associated tables for additional details.

2017-08-27 | MSV000081483 | MassIVE

Comparing the Transcriptomes of Marf1 wildtype (WT) oocytes with those of Marf1-genetrap (GT-Mut) and Marf1-D272 mutant(D272-Mut) oocytes by RNA-Seq Analysis

Project description:The goal of this study is to reveal the globle changes of oocyte transcriptome after mutations of Marf1 either by gene trap or knockin of point mutation by comparing the corresponding transcriptomes via RNA-Seq Analysis.

2018-11-14 | GSE109196 | GEO

Comparison of transcriptomes between Marf1+/+ (WT) and Marf1 ENU/ENU (Mutant) fully-grown oocytes (FGO)

Project description:Marf1 (MUT) female mice are infertile and the meiosis of the oocytes are arrest at prophase I. We thought to identify the potential causes of the meiotic arrest phenotype in the mutant oocytes by comparing the transcriptomes of the WT and mutant fully-grown oocytes (from 23-d old mice) that are transcriptional silent. We compared the transcriptomes of WT and MUT FGOs. 3 individual oocyte samples of each genotype (WT and MUT).

2012-03-30 | E-GEOD-31985 | biostudies-arrayexpress

Comparison of transcriptomes between Marf1+/+ (WT) and Marf1 ENU/ENU (Mutant) fully-grown oocytes (FGO)

2012-03-31 | GSE31985 | GEO

Comparing the Transcriptomes of Marf1-genetrap (GT) oocytes with those microinjected with mRNAs for wild type MARF1 (GTWT) or D272-mutated MARF1 (GTD272) by RNA-Seq Analysis

Project description:Comparing the Transcriptomes of Marf1-genetrap (GT) oocytes with those microinjected with mRNAs for wild type MARF1 (GTWT) or D272-mutated MARF1 (GTD272) by RNA-Seq Analysis

| PRJNA430084 | ENA

Chromatin immunoprecipitation of human HEK293 cells with flag-tagged IMP1 antibody

Project description:Isolation of IMP1 bound mRNAs. Flag-tagged IMP1 was expressed in HEK293 cells. Flag tagged IMP1 was immunoprecipitated and mRNAs isolated. As controls HEK293 cells that do not express Flag-tagged IMP1 was included.

2006-12-31 | E-MEXP-841 | biostudies-arrayexpress

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [PAR-CLIP]

Project description:Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. Close to one third of these proteins, were neither previously annotated nor could be functionally predicted to bind RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of unexpected mRNA-binders with novel molecular functions participating in combinatorial post-transcriptional gene-expression networks. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129M-bM-^@M-^S141, with HEK293 cell lines stably expressing HIS/FLAG/HA-tagged ALKBH5, C17orf85, C22orf28, CAPRIN1, and ZC3H7B. We used 4-thiouridine (4SU) to enhance the crosslink and generated two PAR-CLIP cDNA libraries per protein.

2012-06-01 | E-GEOD-38201 | biostudies-arrayexpress

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