Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

ABSTRACT: CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

PROVIDER: PRJNA860969 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20351906_1.fastq.gz	Fastqsanger.gz
	SRR20351906_2.fastq.gz	Fastqsanger.gz
	SRR20351907_1.fastq.gz	Fastqsanger.gz
	SRR20351907_2.fastq.gz	Fastqsanger.gz
	SRR20351908_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

Project description:We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis in chemical reprogramming, we compared reprogramming efficiency for CD-treated, Rxra-OE and shE3 cells. We then performed RNA-seq for 3 different treatments of 6 samples.

2023-05-03 | GSE208765 | GEO

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

Project description:We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis in chemical reprogramming, we construct Flag-Rxra-OE cells. We performed Flag-Rxra CUT&Tag with reprogramming intermediate, also we performed CUT&Tag with or without CD treatment for reprogramming intermediates.

2023-05-03 | GSE208767 | GEO

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

Project description:CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

| PRJNA860971 | ENA

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

Project description:CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

| PRJNA860973 | ENA

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

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

2023-05-03 | GSE208771 | GEO

ChIP-seq Profiling of RXRα in Proliferating C2C12 Myoblasts

Project description:In this dataset, we present ChIP-seq profiling of RXRα in proliferating C2C12 myoblasts, which serves as an extension of Series GSE94558. The overall data provides genome-wide occupancy of RXRα in normal myoblast proliferation.

2024-10-31 | GSE279060 | GEO

The RNA Exosome Promotes Transcription Termination of backtracked RNA Polymerase II

Project description:Large fractions of genomes are expressed in most eukaryotic cells, generating a diverse repertoire of protein-coding and non-coding transcripts. With such complexity, and as the number of mRNA molecules per cell are often low, it is clear that errors anywhere in the gene expression process could have profound consequences on cellular functions. The exosome is a conserved RNA degradation machine that plays a fundamental role in monitoring the quality of gene expression in the nucleus. The current view is that the nuclear exosome constantly scrutinizes transcription and contributes to post-transcriptional turnover of faulty mRNAs. Yet, how nuclear RNA surveillance by the exosome is coordinated with transcription is still unknown. Here we show that the exosome can directly target the transcription machinery by terminating transcription events associated with paused and backtracked RNA polymerase II (RNAPII), contrary to the notion that the exosome acts exclusively on RNAs that have been released by RNAPII. Our data support a mechanism by which RNAPII backtracking provides a free RNA 3' end for the core exosome, resulting in transcription termination with the concomitant degradation of the associated transcript. These findings uncover a mechanism of co-transcriptional RNA surveillance whereby termination of transcription by the exosome prevents aberrant read-through RNAs and transcriptional interference at neighboring genes.

2014-09-20 | E-MTAB-2237 | biostudies-arrayexpress

RNA-seq of Schizosaccharomyces pombe nuclear RNA exosome mutants

Project description:Nuclear 3’ to 5’ nuclease RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given the large number of RNA species and intervening RNA processing factors. Here we analysed changes in the poly(A)+ RNA proteins interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. Our data demonstrate a functional connection between Rrp6 and Mtl1 in controlling processing and levels of multiple protein-coding and non-coding transcripts. Furthermore, we show that exosome mutants accumulate components of U1 and U2 snRNPs and show depletion of NTC components from RNA suggesting that the stage prior to the activation of the spliceosome represents a critical quality control step. We have also identified potential new RNA binding factors involved in exosome regulation, including a zinc-finger protein called Mub1 that controls levels of selected transcripts encoding for proteins implicated in stress response. Collectively, our data have provided a global view of RNA metabolism alterations in exosome deficient cells and revealed RNA binding proteins that may act as novel exosome cofactors.

2020-04-17 | GSE148799 | GEO

Activation of RXRα reprograms chromatin accessibility to protect against acute kidney injury [ChIP-seq]

Project description:Purpose: To explore whether the differences in chromatin occupancy of RXRα correlate with distinct gene expression in PTCs of MI and SI Methods: Proximal tubules were isolated for RXRα ChIP-seq Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (mm10). Conclusions: We mapped the chromatin occupancy of RXRα.

2022-11-05 | GSE197813 | GEO

RNA-seq Facilitates Quantitative Analysis of Wild Type and RXRα-silenced HepG2-NTCP Cell Transcriptomes

Project description:The goals of this study are to check mRNA levels of genes and pathways regulated by RXRα knocking down, and figure out their influences to HBV infection. The mRNA profiles of wild-type (WT) and RXRα knockdown (RXRα-KD) HepG2-NTCP cells were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the gene level with TopHat followed by Cufflinks. Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome. We find arachidonic acid synthesis, retinol metabolism pathways and serveral other genes are regulated by RXRα knockdown. We also revealed that reduced gene expression in arachidonic acid (AA)/eicosanoids biosynthesis pathways, in particular one of the AA synthases Phospholipase A2 Group IIA (PLA2G2A), is associated with increased HBV infection. Moreover, we also found exogenous treatment of AA inhibits HBV infection. These data implicate the participation of AA/eicosanoids biosynthesis pathways in the regulation of HBV infection, and point to a novel potential strategy for host-targeted therapies against HBV.

2017-12-21 | GSE108366 | 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