Transcription profiling of mouse Pac1+/+ versus Pac1-/- TG-macrophages treated with LPS - 6h
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Charles Reay Mackay
PROVIDER: E-GEOD-3993 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series:; GSE3993: Pac1+/+ versus Pac1-/- TG-macrophages_LPS 6h; GSE3994: Pac1+/+ versus Pac1-/- BMMCs_IgE-DNP 2 h Experiment Overall Design: Refer to individual Series
2008-06-12 | E-GEOD-4014 | biostudies-arrayexpress
Project description:Bone marrow-derived mast cells were differentiated over 4-6 weeks using bone marrow from Pac-1+/+ and Pac1-/- littermate mice. Cell purity was 99% c-kit and Fc epsilon receptor positive as assessed by flow cytometry. Cells were stimulated by Fc epsilon receptor crosslinking using IgE-DNP/HSA for sensitization for 18 hours and DNP-HSA antigen for crosslinking for 2 hours. Gene transcript abundance was determined and scaled to 150 using alogorithms in MicroArray Analysis Suite Software 5.0 (Affymetrix). Experiment Overall Design: Two genechips on independent mBMMC cultures was performed. The signal data of the .CEL files for the four Affymetrix 430A chips (2 Pac1+/+ and 2 Pac1â/â) were normalised using the RMA method 49. The ebayes function implemented in the version 1.3.12 of the Limma package (2003) of Bioconductor was used to analyse the data and P-values were adjusted for multiple testing. After conversion from logged values to the original intensities, the data was filtered to remove probe sets with mean, non-logged, intensities below 100. Transcripts with p-values less than 0.05 were considered different from Pac1+/+.
2008-06-12 | E-GEOD-3994 | biostudies-arrayexpress
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
Project description:Macrophages are a major cellular component of all inflammatory situations, generating proinflammatory cytokines such as TNF-alpha, IL-1, and IL-6 that are central to the initiation and maintenance of inflammation. To determine whether the tumor suppressor ARF plays a role in inflammatory gene expression, we used an 84-gene RT2 PCR array to examine the expression of inflammation-associated genes in WT and ARF-deficient macrophages treated with the TLR4 ligand LPS. Peritoneal macrophages from WT and ARF-deficient mice were obtained and treated with LPS (200ng/ml) for 4 hours. WT control (without stimulation n=4), WT LPS (n=4), ARF Control (n=4), ARF LPS (n=4)
2011-09-29 | E-GEOD-32446 | biostudies-arrayexpress
Project description:Vascular disrupting agents (VDA) represent a novel approach to the treatment of cancer, resulting in collapse of tumor vasculature and tumor death. 5,6-Dimethylxanthenone-4-acetic acid (DMXAA) is a VDA currently in advanced Phase II clinical trials, yet its precise mechanism of action is unknown despite extensive preclinical and clinical investigations. The data presented herein demonstrate that DMXAA is a novel and specific activator of the TBK1-IRF-3 signaling pathway. DMXAA treatment of primary murine macrophages resulted in robust IRF-3 activation, a ~750-fold increase in IFN-beta mRNA and, in contrast to the potent Toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS), signaling was independent of mitogen-activated protein kinase (MAPK) activation and elicited minimal NF-kappaB-dependent gene expression. DMXAA-induced signaling was critically dependent on the IRF-3 kinase, TBK1, and IRF-3, but MyD88-, TRIF-, IPS-1/MAVS-, and IKKbeta-independent, thus excluding all known TLRs and cytosolic helicase receptors. DMXAA pretreatment of murine macrophages induced a state of tolerance to LPS and vice versa. In contrast to LPS stimulation, DMXAA-induced IRF-3 dimerization and IFN-beta expression were inhibited by salicylic acid (SA). These findings detail a novel pathway for TBK-1-mediated IRF-3 activation and provide new insights into the mechanism of this new class of chemotherapeutic drugs. Experiment Overall Design: Microarray analysis was carried out using Affymetrix® mouse array 430A_2 exposed to total RNA prepared from C57BL/6J or IFN-beta-/- macrophages that had been treated with medium alone or DMXAA for 3 h. Fold-induction was calculated using Affymetrix® GeneChip® Operating Software. A >3-fold increase or decrease between inducible and basal mRNA levels was set as the criteria for inclusion of a gene as modulated.
2008-06-15 | E-GEOD-7194 | biostudies-arrayexpress
Project description:Biologic functions involved in innate immune response of macrophages rely on the precise regulation of kinds of immune molecular. In the virus infection procession, the macrophages are activated following a tightly controlled genetic programme where specific sets of genes are up-regulated or down-regulated. We used microarrays to detail the global programme of gene expression underlying VSV infection and identified distinct classes of up-regulated and down-regulated genes during this process. Mouse peritoneal macrophages were selected with/without VSV infection for 8 hours for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression profiles. We selected macrophages according to VSV infection at two time-points: uninfected macrophage(control) and VSV infected for 8 hour macrophages(VSV).
2012-07-23 | E-GEOD-39620 | biostudies-arrayexpress
Project description:Lipopolysaccharide (LPS), a Toll-like receptor (TLR) 4 ligand, induces the expression of various genes including proinflammatory cytokines, and the expression is modified by the presence of Zc3h12a. We used microarrays to examine influence of Zc3h12a deficiency in LPS-inducible gene expression. Experiment Overall Design: Peritoneal macrophages from wild-type and Zc3h12a-/- mice were stimulated with LPS for 0, 1, 2 and 4 hours, followed by RNA extraction. Then hybridization on affymetrix microarrays was performed.
2009-03-01 | E-GEOD-14891 | biostudies-arrayexpress
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
Project description:Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Using a combination of genome-wide and gene-specific approaches, we provide evidence that rather than representing off/on transitions, Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early (I/E) and late response genes results from a sequential process in which signal-independent factors, exemplified by Gabpa, initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by the use of distinct sets of signal-dependent transcription factors, preferential binding of TBP and basal enrichment for RNA Pol II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. NCoR/SMRT co-repressor complexes are unexpectedly found to be associated with H3K4me3-positive promoters of TLR4-responsive genes that exhibit a broad range of basal expression levels, implying a dynamic, rather than static role in regulation of gene expression. Collectively, these findings reveal mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses. ChIP-Seq, Total RNA-Seq, Gro-Seq, and gene expression profiling was performed in macrophages treated with Kdo2 Lipid A. Control samples for H3K4me3 and Input in Macrophages and B cells, in addition to control microarray data are included in GEO accession# GSE21512
2011-01-01 | E-GEOD-23620 | biostudies-arrayexpress
Project description:Akirin2 is an evolutionally conserved nuclear protein involved in the regulation of a set of inflammatory gene expression in various cell types. We used microarrays to examine the effect of Akirin2 deficiency in LPS-inducible gene expression in macrophages Peritoneal macrophages from wild-type and LysM-Cre+;Akirin2fl/fl mice were stimulated with LPS for 0, 2 and 4 hours, followed by RNA extraction and microarray analysis.
2014-07-11 | E-GEOD-59319 | biostudies-arrayexpress