Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from liver samples overxpressing either the GFP or Phf2

ABSTRACT: The GFP or Phf2 were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later. We used microarray analysis to detail the global programme of gene expression underlying Phf2 overexpression and identified distinct classes of up and down regulated genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE61575 | GEO | 2015/10/01

SECONDARY ACCESSION(S): PRJNA261519

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression data from liver samples overxpressing either the GFP or ChREBP

Project description:The GFP or ChREBP were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later. We used microarray analysis to detail the global programme of gene expression underlying ChREBP overexpression and identified distinct classes of up and down regulated genes.

2015-10-01 | GSE61576 | GEO

Expression data from liver samples overexpressing either GFP or ChREBP

Project description:The GFP or ChREBP were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later. We used microarray analysis to detail the global program of gene expression underlying ChREBP overexpression and identified distinct classes of up and down regulated genes.

2022-04-15 | GSE159517 | GEO

QuantSeq analysis in the hippocampus of WT and PHF2 t/g mice

Project description:Long-term memory formation is attributed to experience-dependent gene expression. Dynamic changes in histone methylation status are essential for epigenetic regulation of memory consolidation-related genes. Here, we demonstrated that plant homeodomain finger protein 2 (PHF2) histone demethylase is upregulated in the mouse hippocampus during experience and plays an essential role in memory formation. QuantSeq analysis was performed to examine differential gene expression in the hippocampus of WT and PHF2 t/g mice. Transgenic mice were created by injecting the CMV-Flag-PHF2 vector into fertilized eggs from C57BL6 mice. Transgenic lines were established from 9 founders that were identified via PCR-based genotyping. Among the transgenic lines, mice with high PHF2 expressed brains were singled out for breeding. First, selected heterozygote males were bred with heterozygote females which produced homozygote, heterozygote and wild littermates. Since it is difficult to differentiate between hetero and homo mice with genotyping, we separated homo mice from hetero mice by breeding each of hetero and homo mice with wild type mice and confirming the genotypes of their offspring. In other words, hetero mice bred with wild type mice would have both wild type and hetero genotype of offspring, while homo mice bred with wild type mice would only have hetero genotype of offspring. Through this process, we particularly selected the homo mice and this transgenic line was used and maintained for this experiment.

2019-07-27 | GSE129148 | GEO

Transcriptome analysis in skeletal muscle conditional Phf2 KO gastroceiumus muscle in male mice

Project description:To evaluate the role of PHF2 in skeletal muscle, we generated skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by CUT&RUN-sequencing.

2026-02-23 | GSE314843 | GEO

Transcriptome analysis in skeletal muscle conditional Phf2 KO gastrocnemius muscle in male mice

Project description:To evaluate the role of PHF2 in skeletal muscle, we generated skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by CUT&RUN-sequencing.

2026-02-23 | GSE290665 | GEO

Transcriptome analysis in skeletal muscle conditional Phf2 KO gastroceiumus and soleus muscles in male mice

Project description:To evaluate the role of PHF2 in skeletal muscle, we generated skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by RNA-sequencing.

2026-02-23 | GSE290611 | GEO

Transcriptome analysis in PHf2 KO C2C12 cells

Project description:To evaluate the role of Phf2 in C2C12 myotube, we generated Phf2 KO C2C12 cells and analyzed the transcriptome by RNA-sequencing.

2024-02-29 | GSE226618 | GEO

ChIP-seq experiment of PHF2 and H3K9me2 in NSCs

Project description:Histone H3 lysine 9 methylation (H3K9me) is essential for cellular homeostasis; however, its contribution to development is not well established. Here, we demonstrate that the H3K9me2 demethylase PHF2 is essential for neural progenitor proliferation in vitro and for early neurogenesis in the chicken spinal cord. Using genome-wide analyses and biochemical assays we show that PHF2 controls the expression of critical cell cycle progression genes, particularly those related to DNA replication, by keeping low levels of H3K9me3 at promoters. Accordingly, PHF2 depletion induces R-loop accumulation that leads to extensive DNA damage and cell cycle arrest. These data reveal a role of PHF2 as a guarantor of genome stability that allows proper expansion of neural progenitors during development.

2019-09-10 | GSE122263 | GEO

The epigenetic reader Phf2 is positioned in the genome by cohesin

Project description:Eukaryotic genomes are assembled into chromatin by histones and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs) but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF, decreases the number of short cohesin loops, but increases the length of heterochromatic B compartments. These results suggest that Phf2 is an ‘epigenetic reader’, which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation.

2024-12-19 | GSE281657 | GEO

Interactome analysis of PHF2 using LC-MS combined with an immunoprecipitation assay

Project description:PHF2 demethylates lysine 9 in histone 3 and acts as a tumor suppressor. In liver pathogenesis, PHF2 has dual effects. PHF2 induces simple hepato-steatosis by epigenetically coactivating ChREBP. When lipid accumulation goes serious, it protects the liver from fibrogenesis by facilitating Nrf2 activity, a major transcription factor in the defense against oxidative stress during non-alcoholic fatty liver disease. However, little is known regarding the functions of PHF2 in liver cancer cells. Therefore, to investigate the possible roles of PHF2 and find new interacting proteins, we performed an LC-MS/MS assay combined with an immunoprecipitation assay.

2023-10-18 | PXD044277 | Pride

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