Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of 8-oxodG and gH2AX in growing MCF10A cells and MEFs

ABSTRACT: 8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Several thousand residues of 8-oxodG spread constitutively in the genome of human cells, but their genomic distribution has not yet been characterized. Here, by using OxyDIP-Seq, a highly sensitive methodology that uses high-throughput sequencing, we report the first genome-wide distribution of 8-oxodG in human cells, using the non-tumorigenic epithelial breast cells MFC10A. Results were compared with those we obtained in mouse embryo fibroblasts. OxyDIP-Seq revealed sites of 8-oxodG accumulation overlapping with gH2AX ChIP-Seq signals within gene bodies of long transcribed genes.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE100234 | GEO | 2018/11/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide mapping of 8-oxodG in G0-arrested MCF10A cells

Project description:8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Here, by using OxyDIP-Seq, we report the genome-wide distribution of 8-oxodG in human MCF10A cells arrested in G0.

2020-04-02 | GSE137929 | GEO

Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

Project description:8-Oxo-7,8-dihydro-2’-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs which may in turn stimulate the formation of G4s at PQSs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.

2021-10-09 | GSE181312 | GEO

Peripheral blood lymphocytes with different levels of gH2AX foci and micronuclei

Project description:Transcriptional profiling of peripheral blood lymphocytes with different levels of gH2AX foci and micronuclei after 0 and 2 Gy of gamma-rays. The aim was to identify differentially expressed genes, associated with level of gH2AX and micronuclei.

2017-03-25 | GSE97000 | GEO

Genome-wide mapping of 8-oxodG and gH2AX in growing MCF10A cells and MEFs

Project description:Genome-wide mapping of 8-oxodG and gH2AX in growing MCF10A cells and MEFs

| PRJNA391133 | ENA

Robertsonian translocations modify genomic distribution of gH2AX and H3.3 in mouse germ cells

Project description:Purpose: determine if gH2AX and H3.3 are enriched at unsynapsed regions of chromosomes involved in translocations in mouse germ line (meiotic prophase I) Methods: testes were isolated from 4-week or 6-week old heterozygous carriers of a single Robertsonian translocation RB(8;12) or 3 Robertsonian translocations RB(8;12), RB(1;3) and RB(9;14) and controls. ChIP assays were conducted as described in Smagulova 2011. Experiments done in triplicate. Results: We find enrichment of gH2AX in the proximal gene-rich regions of translocation-associated chromosomes and reduced enrichment of gH2AX and H3.3 at sex chromosomes

2016-11-19 | GSE75221 | GEO

Genome wide mapping of gH2AX in quiescent and irradiation-induced senescent human fibroblasts

Project description:We observe preferential accumulation of gH2AX at chromosome ends upon irradiation comparison of quiescent vs senescent human fibroblasts

2012-03-13 | E-GEOD-35884 | biostudies-arrayexpress

Genome wide mapping of gH2AX in quiescent and irradiation-induced senescent human fibroblasts

Project description:We observe preferential accumulation of gH2AX at chromosome ends upon irradiation

2012-03-13 | GSE35884 | GEO

Genome-wide DNA damage response following ionizing radiation

Project description:H2AX phosphorylation at Ser139 (gH2AX) is an early key event of the DNA damage response (DDR) following DNA double strand breaks (DSB) induction. Although gH2AX distribution has been extensively used as a damage marker, genome-wide investigation of the subsequent DNA repair has been poorly addressed. Here we present ChIP-Seq-based distributions of Histone H3, H2AX and gH2AX under physiological conditions in HeLa cells. Additionally the same histones were studied after a single exposure to 10 Gy X-ray at 0.5, 3 and 24 hours post irradiation

2017-04-17 | GSE60526 | GEO

Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA

Project description:We investigated the nuclear topography, organization and genome-wide gH2AX distribution of unrepaired DNA in rat cortical neurons 15 dyas upon X-Ray ionizing adiation (4Gy). Unrepaired DNA is confined in persistent DNA damage foci which would help preserving genome integrity. ChIp-seq analysis revealed a number of genomic regions enriched in gH2AX. Some of these regions are in close proximity to genes encoding essential proteins for neuronal function and human neurodegenerative disorders.

2019-03-23 | GSE112930 | GEO

Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

Project description:Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

| PRJNA751557 | ENA

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