Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from mouse peritoneal macrophages

ABSTRACT: 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).

ORGANISM(S): Mus musculus

SUBMITTER: weilin chen

PROVIDER: E-GEOD-39620 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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Expression data from mouse peritoneal macrophages

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