Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Macrophage samples from the HMDP

ABSTRACT: Identify genes involved in regulation of inflammatory responses and gene-environemnt interactions, in macrophages from a set of mouse inbred strains termed the HMDP. The HMDP is a genetically diverse mapping panel comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010. GWAS for expression in primary macrophages of mouse inbred strains. Macrophages were exposed to bacterial lipopolysaccharide (LPS), oxidized lipids (OxPAPC) or control treatment conditions.

ORGANISM(S): Mus musculus

SUBMITTER: Calvin Pan

PROVIDER: E-GEOD-38705 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages.

Orozco Luz D LD Bennett Brian J BJ Farber Charles R CR Ghazalpour Anatole A Pan Calvin C Che Nam N Wen Pingzi P Qi Hong Xiu HX Mutukulu Adonisa A Siemers Nathan N Neuhaus Isaac I Yordanova Roumyana R Gargalovic Peter P Pellegrini Matteo M Kirchgessner Todd T Lusis Aldons J AJ

Cell 20121001 3

Many common diseases have an important inflammatory component mediated in part by macrophages. Here we used a systems genetics strategy to examine the role of common genetic variation in macrophage responses to inflammatory stimuli. We examined genome-wide transcript levels in macrophages from 92 strains of the Hybrid Mouse Diversity Panel. We exposed macrophages to control media, bacterial lipopolysaccharide (LPS), or oxidized phospholipids. We performed association mapping under each condition ...[more]

PMID: 23101632

Similar Datasets

Gonadal Adipose Tissue Profiling In HMDP (high-fat/high-sucrose diet)

Project description:Identify genes in the gonadal adipose tissue whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HMDP comprises classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Parks et al Cell Metabolism 2015. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness. GWAS for expression of gonadal adipose tissue in inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks

2015-01-08 | E-GEOD-64768 | biostudies-arrayexpress

Liver Profiling In HMDP (high-fat/high-sucrose diet)

Project description:Identify genes in the liver whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HMDP comprises classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Parks et al Cell Metabolism 2015. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness. GWAS for expression of liver in inbred strains fed chow diet for 8 weeks followed by high-fat/high-sucrose diet 8 weeks

2015-01-08 | E-GEOD-64769 | biostudies-arrayexpress

Aorta profiling HMDP

Project description:Identify genes in the aorta whose expressions under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HDMP is comprised of classical inbred and recombinant inbred wild-type mice. The RMA values of genes were used for genome-wide association as described in Bennett et al. Genome Research 2010 (PMID 20054062). These data were used to identify candidate genes at loci associated with atherosclerosis. Genome-wide association study (GWAS) for expression in aorta of inbred strains.

2012-11-18 | E-GEOD-38120 | biostudies-arrayexpress

Evidence for the importance of OxPAPC interaction with cysteines in regulating endothelial cell function

Project description:Oxidation products of 1-palmitoyl-2-arachidonoyl-sn-glycerol-2-phosphatidylcholine (PAPC), referred to as OxPAPC, accumulate in atherosclerotic lesions and regulate over 1000 genes in human aortic endothelial cells (HAEC). We previously demonstrated that OxPAPC covalently binds to a number of proteins in HAEC. The goal of these studies was to gain insight into the binding mechanism and determine if binding regulates activity. In whole cells N-acetylcysteine inhibited gene regulation by OxPAPC, and blocking cell cysteines with N-ethylmaleimide strongly inhibited OxPAPC binding. Using MS, we demonstrate that most of the binding of OxPAPC to cysteine is mediated by PEIPC. We also show that OxPAPC binds to a model protein, H-Ras, at cysteines previously shown to regulate activity in response to 15dPGJ2. This binding was observed with recombinant protein and in cells overexpressing H-Ras. 15dPGJ2 and OxPAPC increased H-Ras activity at comparable concentrations. Using microarray analysis, we demonstrate a considerable overlap of gene regulation by OxPAPC and 15dPGJ2 in HAEC, suggesting that some effects attributed to 15dPGJ2 may also be regulated by OxPAPC since OxPAPC lipids and 15dPGJ2 both accumulate in inflammatory sites. Overall, we provide evidence for the importance of OxPAPC-cysteine interactions in regulating HAEC function. Control, OxPAPC, and 15dPGJ2-treated HAECs Samples. 'Control' is media (1%FBS, 99%M199)-only treated HAECs. 15dPGJ2 and OxPAPC are treated with those respective compounds in media.

2012-02-14 | E-GEOD-35709 | biostudies-arrayexpress

Epididymal Adipose Tissue Profiling In HMDP

Project description:Identify genes in the epididymal adipose tissue whose expression is under genetic regulation in the hybrid mouse diversity panel. The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness. GWAS for expression of epididymal adipose tissue in inbred strains

2013-01-09 | E-GEOD-42890 | biostudies-arrayexpress

Macrophage samples from the HMDP

Project description:Identify genes involved in regulation of inflammatory responses and gene-environemnt interactions, in macrophages from a set of mouse inbred strains termed the HMDP. The HMDP is a genetically diverse mapping panel comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010.

2012-10-26 | GSE38705 | GEO

Hybrid Mouse diversity Panel Liver Expression Profile

Project description:Novel, systems-based approach to mouse genetics. Expression Profiles from 99 strains of inbred and recombinant inbred mice. Most assayed in triplicate. Two of 288 chips were excluded from the final analysis due to low QC scores.

2010-05-19 | E-GEOD-16780 | biostudies-arrayexpress

Expression data of RNA isolated from C57/BL6 mouse aortic endothelial cells (MAECs)

Project description:Our goal is to study the contribution of endothelial, smooth muscle, and macrophage gene expression to early atherosclerosis using vessels from healthy, pre-lesioned, and lesioned mice. To accomplish this, we developed a method to isolate endothelial cells directly from the aorta and quantitate transcripts in RNA isolated from these cells. We performed expression array analysis on RNA isolated directly from the vascular cells of individual control, pre-lesioned, and atherosclerotic mouse aortas. Array expression analysis was not performed on smooth muscle cells or macrophages. RNA from MAEC of pre-lesioned hyperlipidemic and normal-lipidemic mice was isolated, amplified, and arrayed. Mouse aortas were also treated in either media (DMEM) or media containing either LPS, oxLDL, or oxPAPC for 4 hours prior to RNA isolation and amplification. Only samples with a RIN of 7.0 or greater were used for analysis.

2012-07-10 | E-GEOD-39264 | biostudies-arrayexpress

Heart profiling in HMDP (high-fat/high-sucrose diet)

Project description:Identify genes in the heart whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HMDP comprises classical inbred and recombinant inbred wild type mice. The TPM values of genes were used for genome wide association. These data are used to identify candidate genes at loci associated with cardiovascular traits.

2022-01-31 | GSE194198 | GEO

Skeletal muscle profiling in HMDP (high-fat/high-sucrose diet)

Project description:Identify genes in the skeletal muscle whose expression is under genetic regulation in the Hybrid Mouse Diversity Panel (HMDP). The HMDP comprises classical inbred and recombinant inbred wild type mice. The neqc-normalized values of genes were used for genome wide association. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness.

2015-01-13 | GSE64908 | GEO

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