Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of wild type, Atf3(-/-), Ticam1(-/-), MyD88(-/-) and CREM(-/-) murine bone marrow-derived macrophages stimulated with purified Toll-like receptor agonists after 0-48 hours

ABSTRACT: Time course data from purified Toll-like receptor agonist-stimulated wild_type and knockout murine bone marrow-derived macrophages were collected to investigate the transcriptional network in TLR-activated macrophages.

ORGANISM(S): Mus musculus

SUBMITTER: Stephen Ramsey

PROVIDER: E-TABM-310 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

Ramsey Stephen A SA Klemm Sandy L SL Zak Daniel E DE Kennedy Kathleen A KA Thorsson Vesteinn V Li Bin B Gilchrist Mark M Gold Elizabeth S ES Johnson Carrie D CD Litvak Vladimir V Navarro Garnet G Roach Jared C JC Rosenberger Carrie M CM Rust Alistair G AG Yudkovsky Natalya N Aderem Alan A Shmulevich Ilya I

PLoS computational biology 20080321 3

Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a tran ...[more]

PMID: 18369420

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Project description:Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipid-loaded macrophages in the arterial wall. Intimal macrophages internalize modified lipoproteins such as oxidized LDL (oxLDL) through scavenger receptors, leading to storage of excess cholesteryl esters in lipid bodies and a "foam cell" phenotype. In addition, stimulation of macrophage Toll-like receptors (TLRs) has been shown to promote lipid body proliferation. We investigated the possibility that there are transcriptional regulators that are common to both pathways for stimulating foam cell formation (modified lipoproteins and TLR stimulation), and identified the transcription factor ATF3 as a candidate regulator. In this specific microarray study, we re-analyzed a subset of the data from a 2006 microarray experiment (Gilchrist et al., Nature, 441:173-178, 2006) in which wild-type and Atf3-/- murine macrophages were stimulated with LPS. The goal of this analysis was to identify genes whose LPS responses are significantly affected by loss of ATF3 in macrophages, using up-to-date genome annotations. The raw microarray data files included in this submission were originally released to the public as a part of a larger microarray dataset that accompanied the Gilchrist et al. study (ArrayExpress accession # E-TABM-102). These data were re-analyzed using the CustomCDF v13 ENSG probesets as a part of a transcriptomic study of the response of macrophages to stimuli, including LPS, that induce foam cell formation (see GSE32358 and GSE32359). In the Gilchrist study, the experiment design was as follows: Female mice of the indicated strains were sacrificed at 8-12 weeks of age, and macrophages were derived from the femoral bone marrow using rhM-CSF. On day six, macrophages were plated and LPS introduced into the medium as indicated. After four hours, RNA was isolated using Trizol. Labeled cRNA derived from the RNA samples was hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips. For the current study, probe-level instensity data were re-processed using gene-level probesets from the CustomCDF project (ENSG, v13), and are in log2 scale.

Dataset Information

Transcription profiling of wild type, Atf3(-/-), Ticam1(-/-), MyD88(-/-) and CREM(-/-) murine bone marrow-derived macrophages stimulated with purified Toll-like receptor agonists after 0-48 hours

Publications

Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.

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