Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-nucleotide resolution profiling of N6-methyladenosine in SETD2 knockdown HepG2 cells [m6A miCLIP-seq]

ABSTRACT: To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 knockdown and control HepG2 cells by miCLIP-seq, and found the depletion of H3K36me3 by SETD2 silencing globally reduced m6A in the human transcriptome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE121942 | GEO | 2019/02/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Profiling of N6-methyladenosine in mouse embryonic stem cells: Setd2 knockdown and control cells

Project description:Setd2 is the specific methyltransferase of H3K36me3. To understand the global effect of H3K36me3 on m6A modification, we used mouse embryonic stem cells (mESCs) model with doxycycline (Dox)-induced Setd2 knockdown, and performed m6A-IP followed by sequencing in mESCs with or without Dox treatment. We found that depletion of H3K36me3 by Setd2 silencing globally reduced m6A in mouse transcriptome.

2019-02-21 | GSE110322 | GEO

Profiling of N6-methyladenosine in HepG2 cells: SETD2, METTL3, METTL14 or WTAP knockdown and control cells

Project description:SETD2 is the specific methyltransferase of H3K36me3, while METTL3, METTL14 and WTAP are the components of m6A methyltransferase complex. To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 and METTL3, METTL14 or WTAP knockdown HepG2 cells, and found depletion of H3K36me3 by SETD2 silencing globally reduced m6A in human transcriptome. What’s more, most of the SETD2-dependent hypomethylation sites also responded to knockdown of METTL3, METTL14, or WTAP.

2019-02-21 | GSE110320 | GEO

Single-nucleotide resolution profiling of N6-methyladenosine in SETD2 knockdown HepG2 cells [m6A miCLIP-seq]

Project description:Single-nucleotide resolution profiling of N6-methyladenosine in SETD2 knockdown HepG2 cells [m6A miCLIP-seq]

| PRJNA499111 | ENA

Profiling of N6-methyladenosine (m6A) in salt-treated and control Arabidopsis

Project description:In order to gain insight into m6A in control and salt stress, we performed an miCLIP-sequencing experiment in control and salt treated plants

2018-11-09 | GSE116334 | GEO

m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

Project description:GP61-primed effector CD4+ T cells were isolated from Ctrl or Mettl3-deficient SMARTA mice. Total RNAs were extracted with TRIzol reagent, and mRNAs were then isolated with Dynabeads® mRNA purification kit, followed by stardard m6A-miCLIP-SMARTer-seq with some modifications. Raw sequencing reads were aligned to the mouse genome (mm10) with BWA, and then m6A sites were determined.

2021-01-19 | GSE129649 | GEO

Activin/Nodal-dependent N6-methyladenosine (m6A) deposition in human pluripotent stem cells

Project description:This experiment was designed to probe the function of Activin/Nodal signalling in the deposition of m6A in human pluripotent stem cells (hPSCs). hPSCs were cultured in presence of Activin or subjected to short-term inhibition of Activin/Nodal signalling for 2h using the receptor antagonist SB-431542 (IP). The global abundance of m6A was then measured by nuclear-enriched methylated RNA immunoprecipitation followed by deep sequencing (NeMeRIP-seq). Pre-NeMeRIP input RNA was used as control to normalise for the changes in gene expression in the two conditions.

2017-12-26 | E-MTAB-5229 | biostudies-arrayexpress

m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

Project description:m6A modification in effector CD4+ T cells [m6A-miCLIP-seq]

| PRJNA532394 | ENA

Active ribosome profiling in SETD2 or METTL14 knockdown HepG2 cells

Project description:SETD2 is the specific methyltransferase of H3K36me3, while METTL14 is a critical subunit of the m6A methyltransferase complex. To evaluate the effect of SETD2 and METTL14 on translation, we conducted robosome profiling in SETD2 and METTL14 knockdown and control HepG2 cells. Our RNA ribosome profiling revealed that depletion of SETD2 and METTL14 resulted in a global reduction in RNA translation and the changes of translation efficiency were correlated between SETD2 and METTL14 knockdown cells.

2019-02-21 | GSE121952 | GEO

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down

2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress

Nuclear miCLIP and Nuclear NKAP iCLIP

Project description:To identify m6A sites on endogenous nuclear RNAs, we performed miCLIP to identify m6A sites in PANC-1 cells. To identify NKAP binding sites on endogenous nuclear RNAs, we performed iCLIP for flag-tag NKAP to analyze the nuclear RNA binding with NKAP in the same cells.

2019-03-24 | GSE116425 | 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