Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HDAC inhibition by TSA and Butyrate In Flt3L-elicited DC

ABSTRACT: Butyrate induces Treg via HDACi activity Microarray of DC treated with TSA or Butyrate over untreated

ORGANISM(S): Mus musculus

SUBMITTER: Nicholas Arpaia

PROVIDER: E-GEOD-51263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation.

Arpaia Nicholas N Campbell Clarissa C Fan Xiying X Dikiy Stanislav S van der Veeken Joris J deRoos Paul P Liu Hui H Cross Justin R JR Pfeffer Klaus K Coffer Paul J PJ Rudensky Alexander Y AY

Nature 20131113 7480

Intestinal microbes provide multicellular hosts with nutrients and confer resistance to infection. The delicate balance between pro- and anti-inflammatory mechanisms, essential for gut immune homeostasis, is affected by the composition of the commensal microbial community. Regulatory T cells (Treg cells) expressing transcription factor Foxp3 have a key role in limiting inflammatory responses in the intestine. Although specific members of the commensal microbial community have been found to poten ...[more]

PMID: 24226773

Similar Datasets

HDAC inhibition by TSA and Butyrate In Flt3L-elicited DC

Project description:Butyrate induces Treg via HDACi activity

2013-10-15 | GSE51263 | GEO

Unraveling epigenetic changes in A. thaliana calli: Impact of HDAC inhibitors

Project description:The aim was to characterize epigenetic changes in histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings using mass spectrometry-based approach. Increased level of histone H3.3 variant was found to be the most prominent feature of 20-day-old calli, associated with chromatin relaxation. Methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate and trichostatin A, although each HDACi affected the state of post-translational histone modifications in a specific manner.

2024-01-26 | PXD046788 | Pride

Butyrate Study

Project description:Butyrate Study

| PRJEB30292 | ENA

ESC Exposed to Butyrate

Project description:This SuperSeries is composed of the following subset Series: GSE15107: R1 mESC Exposed to Butyrate GSE15109: BG02 hESC Exposed to Butyrate GSE15110: H1 hESC Exposed to Butyrate Refer to individual Series

2009-03-04 | E-GEOD-15112 | biostudies-arrayexpress

Continuous requirement for the T cell receptor for regulatory T cell function

Project description:Foxp3+ regulatory T cells (Treg cells) maintain immunological tolerance and their deficiency results in fatal multi-organ autoimmunity. Although heightened T cell receptor (TCR) signaling is critical for the differentiation of Treg cells, the role of TCR signaling in Treg cell function remains largely unknown. Here we demonstrate inducible ablation of the TCR results in Treg cell dysfunction which cannot be attributed to impaired Foxp3 expression, decreased expression of Treg cell signature genes or altered ability to sense and consume interleukin 2. Rather, TCR signaling was required for maintaining the expression of a limited subset of genes comprising 25% of the activated Treg cell transcriptional signature. Our results reveal a critical role for the TCR in Treg cell suppressor capacity. Array expression of Foxp3-CreERT2 CalphaFL/WT mice

2014-09-08 | E-GEOD-61077 | biostudies-arrayexpress

Inflammation induced repression of Foxp3-bound chromatin in regulatory T cells [microarray]

Project description:The transcription factor Foxp3 is indispensable for the ability of regulatory T (Treg) cells to suppress fatal inflammation. Here, we characterized the role of Foxp3 in chromatin remodeling and regulation of gene expression in actively suppressing Treg cells in an inflammatory setting. Although genome-wide Foxp3 occupancy of DNA regulatory elements was similar in resting and in vivo activated Treg cells, Foxp3-bound enhancers were poised for repression only in activated Treg cells. Following activation, Foxp3-bound sites showed reduced chromatin accessibility and selective H3K27 tri-methylation, which was associated with Ezh2 recruitment and downregulation of nearby gene expression. Thus, Foxp3 poises its targets for repression by facilitating formation of repressive chromatin in regulatory T cells upon their activation in response to inflammatory cues. The supplementary file GSE55705_dt_expr.txt is a matrix for Treg expression data from platform GPL1261 that includes co-normalized data from GSE40685. array expression

2014-04-12 | E-GEOD-55705 | biostudies-arrayexpress

Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [Expression]

Project description:Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis. It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape. Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to pre-accessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers inaccessible in Foxp3- CD4+ cells became accessible upon T cell receptor activation prior to Foxp3 expression with only a small subset associated with several functionally important genes being exclusively Treg cell-specific. Thus, in a late cellular differentiation process Foxp3 defines Treg cell functionality in an “opportunistic” manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape. Array expression. Three cell types with 3-5 replicates each.

2012-09-28 | E-GEOD-40685 | biostudies-arrayexpress

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

Project description:We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. We identified several thousand specific regulatory elements (~10% of total DHS sites) that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid (SAHA) 72-hour treatments. Most of the differential DNase-hypersensitive (DHS) sites display hallmarks of enhancers; including being enriched for non-promoter regions, associated with nearby gene expression changes, and capable of increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 becomes up-regulated and increases binding at opened DHS sites by ChIP-seq with HDACi treatment, but show that increased PU.1 protein levels alone are sufficient for only modest increases in chromatin accessibility. PU.1 knockdown by shRNA failed to block the HDACi-induced chromatin accessibility and expression changes in K562, suggesting factors other than PU.1 are responsible for establishment of active enhancers in the HDACi induced differentiation process.

2016-04-10 | GSE74999 | GEO

Inflammation induced repression of Foxp3-bound chromatin in regulatory T cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-04-12 | E-GEOD-55753 | biostudies-arrayexpress

H1 hESC Exposed to Butyrate

Project description:To assess the effect of sodium butyrate exposure on human ESC grown without culture support for self-renewal (I.e. without conditioned medium and added bFGF) - three groups were compared - H1 culture in feeder conditioned medium vs without conditioned medium in 0.2 mM sodium butyrate vs. grown in sodium butyrate for 4 passages followed by return to conditioned medium conditions for 3 passages. The three groups were grown in triplicate and compared on Agilent whole human genome array

2009-03-05 | GSE15110 | 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