Contact \| News \| Publications \| Site Map
	LIPID Metabolites And Pathways Strategy

About Data Tools Protocols Home
Lipid Classification Scheme \| Component Databases \| Experimental Results

Microarray analysis of LPS responses of thioglycolate-elicited macrophages and counter-regulation by glucocorticoid receptor, PPARγ and LXR-specific ligands

Experimental design

Thioglycollate-elicited macrophages were isolated from wild type or IRF3-deficient mice by peritoneal lavage 3 days following peritoneal injection of 2.5 ml 3% thioglycollate (DIFCO). Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after 5 h the medium was removed and cells were fed with fresh medium containing 0.5% fetal bovine serum. Cells were treated with LPS (Sigma) a concentration of 100 ng/ml or poly I:C (100 ng/ml) in the absence or presence of receptor-specific agonists for the glucocorticoid receptor (dexamethasone), PPARγ (GW7845) or LXR (GW3965) at 1 µM concentrations. Cells were lysed with Trizol (Invitrogen) six hours following LPS or poly I:C treatment and total RNA was purified using RNeasy columns (Qiagen). cRNA was generated from 10 ug total RNA using Superscript (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo). Fragmented cRNA was hybridized to Codelink mouse Uniset 1 microarrays according to manufacture's instructions. Data was analyzed with Microarray Suite (Affymetrix), GeneSpring (Silicongenetics) and in-house software developed as described (Ogawa et al., 2004). Two to four biological replicates were performed for each experimental condition.

Reference: Molecular Determinants of Crosstalk between Nuclear Receptors and Toll-like Receptors Mediating Counter-regulation of Inflammatory Responses. Sumito Ogawa, Jean Lozach, Chris Benner, Gabriel Pascual, Rajendra K. Tangirala, Stefan Westin, Alexander Hoffmann, Shankar Subramaniam, Michael David, Michael G. Rosenfeld, and Christopher K. Glass. Cell, Vol 122, 707-721, 9 September 2005.

Query Interface

Browse Gene Expression Results Gene expression levels were measured for a control (Wild type, no treatment - WT NOTX) plus 10 experimental conditions. Using this interface, you can view results measured for the 100 probes with the highest and lowest fold changes verses control for each of the following treatment conditions:

Treatment conditions - Unigene probes hybridized with each of:

KO (IRF3 (-/-) knock out mice), No treatment (NOTX)
KO + LPS
Wild Type (WT) + LPS
Wild Type (WT) + LPS + DEX
Wild Type (WT) + LPS + LXR
Wild Type (WT) + LPS + PPARg
Wild Type (WT) + PIPC
Wild Type (WT) + PIPC + DEX
Wild Type (WT) + PIPC + LXR
Wild Type (WT) + PIPC + PPARg

WT - Wild-type
KO - IRF3 (-/-) knock out mice
NOTX - no treatment (Control)
LPS - treatment with lipopolysaccharide (binds to TLR4)
PIPC - treatment with PIPC (binds TLR3)
DEX - treatment with dexamethasone (binds to GR)
LXR - treatment with compound GW3965 (binds to LXR)
PPAR/PPARG - treatment with compound GW7845 (binds to PPARγ)

Browse Uniset Mouse 1 Gene Data -- View and sort by LEGACY_PROBE_NAME, MOLECULAR_FUNCTION, BIOLOGICAL_PROCESS, DESCRIPTION, CELLULAR_COMPONENT, with LEGACY_PROBE_NAME's linked to experimental results and gene annotations. Gene annotations include crosslinks to external databases. Note: This page may take several seconds or longer to load, depending on your connection speed -- results are shown in sets of 1000 per page.

Display Record (Results and annotations for given probe / gene)
This search form provides direct access to an individual record of interest when the probe id is known. In the individual probe record, the average of biological replicates is shown, with a link to data for each of the two to four replicates.

Search by Probe ID	(e.g. NM_011841 or NM_011841_PROBE1)

Search by keyword	(e.g. transcription factor OR GO:0003700 OR Mapk7)

Query Uniset Mouse 1 Gene Annotations (linked to results)
(Annotation Fields Searched: LEGACY_PROBE_NAME, OGS (gene name), DESCRIPTION, MOLECULAR_FUNCTION, CELLULAR_COMPONENT)

GOby-rendered report pages.

Click "Term table" to access annotation terms that are enriched among differentially expressed features. Click "Tree View" to display the hierarchical structure of the annotation system with corresponding enrichment likelihoods.

WT NOTX vs KO+LPS	Term table	Tree View (1.8M)
WT NOTX vs KO NOTX	Term table	Tree View (616k)
WT NOTX vs WT+LPS	Term table	Tree View (1.4M)
WT NOTX vs WT+LPS+DEX	Term table	Tree View (1.3M)
WT NOTX vs WT+LPS+LXR	Term table	Tree View (1.7M)
WT NOTX vs WT+LPS+PPARg	Term table	Tree View (1.5M)
WT NOTX vs WT+PIPC	Term table	Tree View (1.4M)
WT NOTX vs WT+PIPC+DEX	Term table	Tree View (1.5M)
WT NOTX vs WT+PIPC+LXR	Term table	Tree View (1.6M)
WT NOTX vs WT+PIPC+PPARg	Term table	Tree View (2.0M)

GOby is a gene annotation tool that identifies statistically overrepresented gene groups, and is available as part of the VAMPIRE Microarray analysis suite.

Reference: VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, and Shankar Subramaniam. Nucleic Acids Research, Nucleic Acids Research 2005 33(Web Server issue):W627-W632; doi:10.1093/nar/gki443

Download Normalized Data

.txt (2.1 MB)
.txt.gz (648 KB)

Explanation of column headers in *normalized data

WT stands for "Wild-type" and KO stand for the "IRF3 (-/-) knock out mice"
NOTX - no treatment (Control)
LPS - treatment with lipopolysaccharide (binds to TLR4)
PIPC - treatment with PIPC (binds TLR3)
DEX, LXR, and PPARγ are always paired with either LPS or PIPC in these experiments since we are studying their effect on inflammation.
DEX - treatment with dexamethasone (binds to GR)
LXR - treatment with compound GW3965 (binds to LXR)
PPAR/PPARG - treatment with compound GW7845 (binds to PPARγ)

All experiments were carried out 6 hours after being treated.

*Reference: Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Sasik et al. Bioinformatics. 2002 Dec;18(12):1633-40