Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis to identify the genes regulated by p53-SET interplay

ABSTRACT: To identify the genes regulated by SET in a p53-dependent manner, the endogenous SET was depleted by siRNA in control or p53 knockout U2OS cells. Total RNA from each sample was extracted and the whole profile of gene expression was analyzed by RNA-seq analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE83635 | GEO | 2016/09/12

SECONDARY ACCESSION(S): PRJNA326537

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Embryonic stem cell differentiation is regulated by SET through interactions with p53 and β‐catenin

Project description:The multifunctional histone chaperone, SET, is essential for embryonic development in mouse. Previously, we identified SET as a factor that is rapidly downregulated during embryonic stem cell (ESC) differentiation, suggesting a possible role in the maintenance of pluripotency. Here, we set out to explore SET’s function and its mechanism in early differentiation. Using liquid chromatography tandem mass spectrometry (LC‐MS/MS), we uncover the factors and complexes, including P53 and β-catenin, by which SET regulates lineage-specification. SET knockout (KO) and shRNA-knockdown experiments for both P53 and β-catenin in SET-KO ESCs reveal that P53 knockdown partially rescues lineage-marker misregulation during differentiation. β-catenin depletion, on the other hand, rescues the elevated Wnt gene expression observed in SET-KO ESCs. Integration of multiple ChIP-seq and RNA-seq datasets reveals a predominantly activating function of SET in gene regulation. Moreover, further analysis reveals a co-regulatory relationship between SET and TCF3, a downstream effector of Wnt-signalling. Overall, we discover a role for both P53 and β-catenin in SET-regulated early differentiation and uncover a potential mechanism for SET function at the β-catenin-TCF regulatory axis.

2020-12-22 | GSE154607 | GEO

Pin1/mutant-p53 jointly controlled genes

Project description:To investigate the specific gene expression program by which mutant-p53 and Pin1 control invasion and metastasis in breast cancer cells, we compared the transcriptomic profile of control, mutant-p53 depleted or Pin1 depleted MDA-MB-231 cells. MDA-MB-231 cells were transfected twice with siRNA against Pin1, p53 or LacZ as a control. Transfections were performed by using Lifofectamine 2000 (Invitrogen) according to manufacture's procedure. Forty-eight hours after second transfection, samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Three biological replicas (A, B, C) were used for each of the three conditions, for a total of 9 samples

2011-05-30 | E-GEOD-26262 | biostudies-arrayexpress

Chromatin immunoprecipitation to determine p53 binding to promoter regions in human U2OS cells without activation of p53

Project description:p53 binding to promoter regions in U2OS cells without activation of p53

2010-01-31 | E-MEXP-2537 | biostudies-arrayexpress

Impact of mutant p53 on TNF-induced gene expression

Project description:MDA-MB-231 are a metastatic triple-negative breast cancer cell line that bears a missense p53 mutation (R280K). We depleted endogenous mutp53 in MDA-MB-231 cells by siRNA transfection, and treated the cells with Tumor Necrosis Factor (TNF)-alpha. Microarray analysis was performed to evaluate the impact of mutant p53 on the transcriptional response triggered by TNFα in these cells. MDA-MB-231 cells transfected with control or p53 siRNA were treated with TNFα for 20 hrs or left untreated. The study comprises four experimental points, each in triplicate.

2014-10-27 | E-GEOD-53153 | biostudies-arrayexpress

Impact of mutant p53 on TNF-induced gene expression

2014-10-27 | GSE53153 | GEO

p53-induced apoptosis is specified by a translation program regulated by PCBP2 and DHX30.

Project description:Activation of p53 by the small molecule Nutlin can result in a combination of cell cycle arrest and apoptosis. The relative strength of these events is difficult to predict, leaving uncertainty as to the therapeutic benefits of Nutlin. Here, we report a new translation control mechanism shaping p53-dependent apoptosis. We performed polysomal profiling in the cell lines SJSA1 and HCT116, of which only the first undergoes robust cell death in response to p53 activation by Nutlin. We establish Nutlin-induced apoptosis in SJSA1 cells to be associated with a set of translationally enhanced mRNAs carrying a newly identified 3’UTR motif which we labeled CG-motif. We identified PCBP2 and DHX30 as interactor proteins of the CG-motif that are more abundant in HCT116 cells compared to SJSA1. The binding of DHX30 to the CG-motif detected in HCT116 cells was shown to be dependent on PCBP2. Interestingly, DHX30 depletion enhances polysome association of CG-motif mRNAs in HCT116 cells, shifting their outcome towards apoptosis. In U2OS, an osteosarcoma-derived cell line that unlike SJSA1 undergoes persistent cell cycle arrest in response to Nutlin, DHX30 is highly expressed and its depletion enhances the expression of CG-motif mRNAs.

2020-03-30 | GSE95024 | GEO

Suppression of p53-mediated senescence by non-canonical NF-kappaB pathway mediated regulation of EZH2 expression

Project description:The NF-kappaB and p53 transcription factors control the expression of complex gene regulatory networks in response to many cell stresses and stimuli. This experiment describes gene expression profiling of cells depleted for EZH2, NF-kappaB2, RelB and p53. We find that EZH2 is the major effector of crosstalk between the alternative NF-kappaB and p53 pathways and acts to suppress cellular senescence. Total RNA was obtained from primary juvenile human dermal fibroblasts 48 hours after transfection with siRNA specific for one, or a targeted combination of the transcription factors, or a scrambled siRNA control.

2014-03-31 | E-MTAB-1593 | biostudies-arrayexpress

Exogenous BRCT-GST of PARP1 bind to wild-type p53. p53 was overexpressed after UV treatment in U2OS.

Project description:Exogenous BRCT-GST in U2OS bind to wild-type p53 in a phosphorylation-dependent manner, after UV treatment. BRCT-GST fusion protected cells from apoptotic cell death and impact of miRNAs responsive to p53 activation.

2024-03-02 | E-MTAB-3628 | biostudies-arrayexpress

Identification of p53-regulated microRNAs in Hapatocellular Carcinoma (HCC).

Project description:p53 suppresses tumor progression and metastasis by regulating a large set of genes and microRNAs. By profiling 92 primary hepatocellular carcinomas (HCCs) and 9 HCC cell lines, we found that p53 upregulates microRNAs including miR-200 and miR-192 family members.

2011-05-11 | GSE28661 | GEO

Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells

Project description:The main goal of this study is to integrate gene expression analysis with ChIP-chip study. To examine the relationship between promoter occupancy and gene expression, we transiently depleted p53 and p73 via small interfering RNA (siRNA) in HCT116-3(6) cells and then performed microarray analysis of 32,000 genes before or after HU treatment using the Phalanx expression array platform. We found that only 6%-14% of p53 and p73 bound promoters at FDRMAP <0.05 exhibited significant changes in mRNA expression when p53 and p73 were simultaneously knocked-down by siRNA. The minimal correlation between binding and regulation of expression is consistent with previous observations of the lack of transcriptional effects at many transcription factor binding sites.

2009-06-30 | GSE12242 | 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