Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells [FAIRE-Seq]

ABSTRACT: We performed global mapping of accessible chromatin in mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq) to analyze the mechanisms of transcriptional regulation during TGF-beta-induced EMT.

ORGANISM(S): Mus musculus

PROVIDER: GSE69364 | GEO | 2017/04/10

SECONDARY ACCESSION(S): PRJNA285318

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

FAIRE-seq analysis of Ras transformed mouse mammary gland epithelial cells transfected with Etv4 and Etv5 siRNAs and stimulated with TGF-beta.

Project description:We performed global mapping of accessible chromatin in mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq) to analyze the mechanisms of transcriptional regulation during TGF-beta-induced EMT.

2017-04-10 | GSE94977 | GEO

Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells

Project description:This SuperSeries is composed of the SubSeries listed below. Epithelial-mesenchymal transition (EMT) is induced by transforming growth factor (TGF)-beta stimulation and facilitates tumor progression. We here performed global mapping of accessible chromatin in the mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq). We also searched for differentially expressed transcription factors by RNA-seq and found that Etv4, an ETS family oncogenic transcription factor, was strongly expressed in EpRas cells. Moreover, chromatin immunoprecipitation (ChIP)-seq showed that Etv4 bound to more than one-third of the accessible chromatin regions in EpRas cells treated with TGF-beta. We found by gene ontology analysis that genes encoding extracellular proteins are the most strongly down-regulated genes by Etv4 and Etv5 siRNAs. These findings suggest a mechanism of transcriptional regulation during TGF-beta-induced EMT that involves alterations of accessible chromatin.

2017-04-10 | GSE69387 | GEO

FAIRE-seq

Project description:Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in U2OS cells detected by SOLiD sequencing

2011-11-03 | E-MTAB-584 | biostudies-arrayexpress

FAIRE-chip in MCF7 and LNCaP

Project description:The compaction degree of chromatin is intimately related to its functionality and active cis-regulatory elements typically exist within open chromatin regions depleted in nucleosomes (Heintzman et al. 2007; Boyle et al. 2008). These domains can be identified using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) that allows for enrichment of nucleosome-depleted genomic regions when cross-linked chromatin is subjected to phenol-chloroform extraction (Nagy et al. 2003; Hogan et al. 2006) Here, chromatin structure was analyzed in MCF7 and LNCaP cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Nagy et al. 2003; Hogan et al. 2006) Keywords: FAIRE-chip

2009-01-07 | GSE11579 | GEO

FAIRE-chip in MCF7 and LNCaP

2010-05-14 | E-GEOD-11579 | biostudies-arrayexpress

FAIRE-seq in Rex1GFPd2 mouse embryonic stem cell line

Project description:Formaldehyde-assisted isolation of regulatory elements (FAIRE) in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

2014-06-24 | E-MTAB-2283 | biostudies-arrayexpress

RNA-sequencing of EpH4 and EpRas cells treated with Etv4 and Etv5 siRNAs and/or TGF-beta.

Project description:We performed RNA-seq analysis in mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) to analyze the mechanisms of transcriptional regulation during TGF-beta-induced EMT.

2017-04-10 | GSE69363 | GEO

Meiotic time course of open chromatin as measured by FAIRE

Project description:To investigate the relationship between chromatin organization and meiotic processes, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae.

2009-07-01 | GSE16163 | GEO

FAIRE-seq in primary human megakaryocytes, erythroblasts and monocytes

Project description:Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. 2010), and reanalyzed these data sets using the same methodology.

2013-04-08 | GSE37916 | GEO

Archival chromatin sequencing in formalin-fixed mouse specimens [FAIRE and Mnase]

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.

2024-03-15 | GSE261169 | 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