Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ATAC-seq]

ABSTRACT: The activity of the regulatory regions was determined by MED1 (a subunit of the Mediator complex) ChIP-seq and chromatin openness was measured using assay for transposase-accessible chromatin with sequencing (ATAC-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE246307 | GEO | 2024/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ChIP-seq]

Project description:In this study, the retinoid and vitamin D pathways were investigated in PMA-differentiated THP-1 cells treated with or without the RARa agonist, AM580, and/or the VDR agonist, 1,25-dihydroxyvitamin D3 (1,25-vitD or calcitriol), using global approaches. Binding regions of RARa and VDR were determined in PMA-differentiated THP-1 cells using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). The gene sets regulated by AM580 and/or 1,25-vitD were identified by RNA-sequencing (RNA-seq). The activity of the regulatory regions was determined by MED1 (a subunit of the Mediator complex) ChIP-seq and chromatin openness was measured using assay for transposase-accessible chromatin with sequencing (ATAC-seq).

2024-12-31 | GSE246308 | GEO

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [RNA-seq]

Project description:In this study, the retinoid and vitamin D pathways were investigated in PMA-differentiated THP-1 cells treated with or without the RARa agonist, AM580, and/or the VDR agonist, 1,25-dihydroxyvitamin D3 (1,25-vitD or calcitriol), using global approaches. Binding regions of RARa and VDR were determined in PMA-differentiated THP-1 cells using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq). The gene sets regulated by AM580 and/or 1,25-vitD were identified by RNA-sequencing (RNA-seq). The activity of the regulatory regions was determined and chromatin openness was measured using assay for transposase-accessible chromatin with sequencing (ATAC-seq).

2024-12-31 | GSE246309 | GEO

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells.

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-12-31 | GSE246310 | GEO

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells.

Project description:Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells.

| PRJNA1032473 | ENA

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [RNA-seq]

Project description:Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [RNA-seq]

| PRJNA1032481 | ENA

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ATAC-seq]

Project description:Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ATAC-seq]

| PRJNA1032482 | ENA

Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ChIP-seq]

Project description:Retonic acid and vitamin D signalling pathways converge at genomic regions co-occupied by RARa and VDR in differentiated THP-1 cells [ChIP-seq]

| PRJNA1032483 | ENA

Knockouts of both Vitamin D receptor (VDR) and its coactivator Med1 enhance epidermal permeability barrier function

Project description:Vitamin D receptor (VDR) is crucial for formation of epidermal permeability barrier and ceramide production, while mediator complex subunit 1 (Med1), a coactivator of VDR, mediates the action of VDR. VDR deficiency compromises epidermal permeability barrier in mice. Hence, we are investigating the dual role of VDR and Med1 in epidermal permeability barrier. Mice with VDR and Med1 specifically deleted in Keratin 14 expressing keratinocytes (DKO) by Cre-lox strategy are utilized. The mice with both floxed VDR and Med1 but no Cre serve as control. The data showed here that knockouts of both VDR and Med1 enhanced epidermal permeability barrier in mice, accompanied by increased expression levels of mRNA for keratinocyte differentiation marker-related proteins, fatty acid and ceramide productions, which all are required for formation of epidermal permeability barrier. Moreover, expression levels of mRNA for ceramide transporter (ABCA12) were also elevated in DKO mice vs. knockout of either VDR or Med1 alone. Collectively, these results demonstrate that knockouts of both VDR and Med1 enhance epidermal permeability barrier function via upregulating expression levels of mRNA for epidermal differentiation marker-related proteins and lipid synthetic enzymes, suggesting additional signaling pathway(s) involve regulatory role of VDR/Med1 in epidermal function.

2020-09-14 | GSE157887 | GEO

Effects of vitamin D on VDR binding in THP-1 cells

Project description:Three independent repeats of ChIP-seq or ChIPmentation with THP-1 cells after treatment with either 1,25(OH)2D3 (VD) or control (EtOH) using antibody against VDR.

2024-09-30 | GSE124056 | GEO

Vitamin D receptor (VDR) target genes in THP-1 monocytic leucemia cells

Project description:The biologically active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is a direct regulator of gene transcription, since it is the only high affinity natural ligand of the transcription factor vitamin D receptor (VDR). Transcriptome-wide analysis of THP-1 human monocyte-like cells had indicated more than 600 genes to be significantly (p < 0.05) regulated after a 4 h stimulation with 1,25(OH)2D3. In this study, we screened of the list of primary vitamin D targets for genes encoding for transcriptional regulators and selected those of the activating transcription factor NFE2 and the transcriptional repressor BCL6. Both genes are under the control of two VDR loci and are the only 1,25(OH)2D3 targets within their respective chromosomal domain. However, NFE2 mRNA was rapidly up-regulated, while the increase of BCL6 expression showed a slower rise. After 24 h incubation of THP-1 cells with 1,25(OH)2D3 more than 1,500 genes responded significantly (p < 0.001), of which 132 where more than 2-fold induced. Public chromatin immunoprecipitation-sequencing datasets suggested that the majority of these genes could be targets of NFE2 or BCL6. In time course experiments we displayed for representative gene examples the specific delayed response of secondary 1,25(OH)2D3 targets and confirmed for the respective chromosomal domains the genomic binding of NFE2, BCL6 and VDR. In conclusion, our study indicated that the physiological response of monocytes to 1,25(OH)2D3 involves the action of NFE2 and BCL6. THP-1 cells were treated 24 h either with 0.1% ethanol (vehicle, control) or 1?,25(OH)2D3 (1,25D)

2015-04-26 | E-GEOD-60102 | biostudies-arrayexpress

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