Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of mouse macrophages stimulated with IL-4 (Biogel and thioglycollate macrophages) (Affymetrix)

ABSTRACT: Analysis of alternative activation of macrophages at gene expression level. The study forms part of a wider study where we compare the effects of IL-4 in different human and mouse macrophages. Our results support the notion that in vitro culture conditions greatly affect the macrophage response to IL-4. Total RNA obtained from Thioglycollate and Biogel elicited peritoneal macrophages exposed to 20 ng/ml of IL-4 for 18 hours. Biogel and thioglycollate elicited macrophages were stimulated with the Th2 cytokine IL-4, for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Fernando Martinez Estrada

PROVIDER: E-GEOD-35436 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide analysis of human macrophages stimulated with IL-4

Project description:This SuperSeries is composed of the following subset Series: GSE5099: Expression Data from Macrophage Maturation and Polarization Experiment GSE35433: Genome-wide analysis of human macrophages stimulated with IL-4 (20ng/ml) (Illumina) GSE35434: Genome-wide analysis of human macrophages stimulated with IL-4 (10ng/ml) (Illumina) GSE35435: Genome-wide analysis of mouse macrophages stimulated with IL-4 (bone marrow macrophages) (Affymetrix) GSE35436: Genome-wide analysis of mouse macrophages stimulated with IL-4 (Biogel and thioglycollate macrophages) (Affymetrix) Refer to individual Series

2012-09-29 | E-GEOD-35495 | biostudies-arrayexpress

MicroRNA expression in thioglycollate and alternatively activated

Project description:Macrophage activation must be tightly controlled to prevent overzealous responses that cause self-damage. MicroRNAs have been shown to promote classical macrophage activation by blocking concomitant anti-inflammatory signals and transcription factors, but can also place restraints on activation by preventing excessive TLR-signalling. In contrast, the microRNA profile associated with alternatively activated macrophages and their role in regulating wound-healing or anti-helminthic responses has not yet been described. Utilizing an in vivo model of alternative activation, in which adult Brugia malayi nematodes are surgically implanted in the peritoneal cavity of mice, we examined the profile of microRNA expression in these alternatively activated macrophages and compared this to alternatively activated IL-4 receptor knockout macrophages and thioglycollate elicited macrophages. Peritoneal macrophages from BALB/c wild type or IL-4 receptor knockout mice were elicited with thioglycollate or using nemtodes (peritoneal implant of Brugia malayi). The latter leads to a population of alternatively activated macrophages. Microarray analysis was used to examine the microRNA profile of WT alternatively activated macrophages (n = 4), IL-4 receptor knockout alternatively activated macrophages (n = 4), WT thioglycollate elicited macrophages (n = 3) and IL-4 receptor knockout thioglycollate elicited macrophages (n = 3).

2012-08-07 | E-GEOD-35047 | biostudies-arrayexpress

miRNA arrays for LPS-activated Akt1+/+ and Akt1-/- macrophages

Project description:MicroRNAs regulated by lipopolysaccharide (LPS) target genes that contribute to the inflammatory phenotype. Here we showed that the protein kinase Akt1, which is activated by LPS, positively regulated miRNAs let-7e, miR-181c but negatively regulated miR-155 and miR-125b. In silico analyses and transfection studies revealed that let-7e repressed Toll-like receptor 4 (TLR4) whereas miR-155 repressed SOCS1, two proteins critical for LPS-driven TLR signalling, which regulate endotoxin sensitivity and tolerance. As a result, Akt1-/- macrophages exhibited increased responsiveness to LPS in culture and Akt1-/- mice did not develop endotoxin tolerance in vivo. Overexpression of let-7e and suppression of miR-155 in Akt1-/- macrophages restored sensitivity and tolerance to LPS in culture and in animals. These results indicate that Akt1 regulates the response of macrophages to LPS by controlling miRNA expression. The data deposited here contain the entire analysis of miRNA profile of Akt1+/+ and Akt1-/- thioglycollate elicited peritoneal macrophages following stimulation with LPS for 3 hours in culture. Thioglycollate elicited macrophages were cultured in complete DMEM medium, stimulated with LPS for 3 hours and RNA was extracted. Samples were analyzed using Taq-man PCR miRNA arrays (Dana Farber microarray Facility).

2009-08-21 | E-GEOD-17421 | biostudies-arrayexpress

Expression data from PPARg WT and KO macrophages

Project description:PPARg is a nuclear receptor that plays an important role in lipid metabolism, homeostasis and immunity. Microarray analysis of gene expression was performed in macrophages from WT and PPARg KO mice. Differentially expressed genes were selected for further analysis. RNA from WT and PPARg KO macrophages was purified for hybridization on Affymetrix microarrays. Peritoneal macrophages were harvest from WT and PPARg KO mice 3 days after intraperitoneal injection of 2.5ml of 3% thioglycollate.

2010-09-24 | E-GEOD-24292 | biostudies-arrayexpress

Effects of acLDL loading on macrophage

Project description:acLDL loading of mouse peritoneal macrophage is an in vitro foam cell model. We have used microarray analysis and proteomics to characterize the effects of acLDL loading on the cells. Macrophages were harvested from the peritoneum of C57Bl/6J mice 5 days after injection of thioglycolate. Thioglycollate elicited macrophage were cultured for 2 days in DMEM + 10%FBS either in the presence or absence of 50 microgram/mL acLDL. 4 indepdendent biological replicates were used for each condition.

2010-12-31 | E-GEOD-19926 | biostudies-arrayexpress

PPARbeta/delta ligand mediated response in primary macrophages

Project description:Primary mouse macrophages from wt and PPARD-/- mice, elucidated with thioglycollate, were exposed to PPARbeta/delta specific ligands and the resulting changes in global gene expression were measured.

2012-01-20 | E-MTAB-512 | biostudies-arrayexpress

Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription

Project description:Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ~3000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. Unexpectedly, we find that enhancer transcription precedes local mono- and di-methylation of histone H3 lysine 4 (H3K4me1/2). H3K4 methylation at de novo enhancers is primarily dependent on the histone methyltransferases Mll1, Mll2/4 and Mll3, and is significantly reduced by inhibition of RNA polymerase II elongation. Collectively, these findings suggest an essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts. ChIP-Seq and Gro-Seq profiling was performed in thioglycollate-elicited peritoneal macrophages, PU.1-/- and PUER cells treated as indicated.

2013-08-09 | E-GEOD-48759 | biostudies-arrayexpress

Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct

Project description:Macrophages adopt an alternatively activated phenotype (AAM) when activated by IL-4. While these AAMs can be derived from local proliferation of resident tissue macrophages or recruited inflammatory monocytes, it is not known whether these different AAMs are phenotypically and functionally distinct. Using microarray analysis of gene expression, we demonstrated that while both monocyte- and tissue-derived AAM expressed high levels of Arg1, Chi3l3 and Retnla, only monocyte-derived AAM upregulated Raldh2 and PD-L2. The distinction between monocyte- and tissue-derived macrophages can, therefore, be made using different phenotypic markers. Gene expression profiling analysis with whole genome microarray of tissue-derived and monocyte-derived macrophages, induced using IL-4c and/or 4% thioglycollate.

2014-02-05 | E-GEOD-54679 | biostudies-arrayexpress

Retinoid X receptors orchestrate osteoclast differentiation and postnatal bone remodeling [SREBP]

Project description:Data from SREBP1c binding to the genome was visualized using Genome Browser (UCSC) in order to test its role in Mafb transcriptional regulation SREBP ChIP was performed in thioglycollate-elicited peritoneal macrophages treated as indicated.

2015-02-04 | E-GEOD-63697 | biostudies-arrayexpress

Retinoid X receptors orchestrate osteoclast differentiation and postnatal bone remodeling [RXR and PPARg]

Project description:Data from nuclear receptors RXR and PPARg binding to the genome was visualized using Genome Browser (UCSC) in order to test their role in Mafb transcriptional regulation RXR and PPARg ChIP was performed in thioglycollate-elicited peritoneal macrophages in basal conditions

2015-02-04 | E-GEOD-63696 | biostudies-arrayexpress

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