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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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JmjD2d-dependence of LPS-induced genes

ABSTRACT: In dendritic cells, expression of the H3K9me3 demethylase JmjD2d is upregulated by LPS stimulation. To identify genes whose induction by LPS depends on JmjD2d activity, we performed a microarray analysis of wild-type and JmjD2d-knockdown dendritic cells, before and after stimulation with LPS. RNA was extracted from three independent cultures of wild-type and JmjD2d-knockdown dendritic cells, before and 4h after stimulation with 100ng/ml LPS. The unstimulated and stimulated wild-type samples, and the stimulated JmjD2d-knockdown samples, were used for microarray analysis.

ORGANISM(S): Mus musculus

SUBMITTER: Dominic van Essen

PROVIDER: E-GEOD-32255 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cell-type-specific control of enhancer activity by H3K9 trimethylation.

Zhu Yina Y van Essen Dominic D Saccani Simona S

Molecular cell 20120501 4

Cell-type-specific control of gene expression is critical for the development of multicellular organisms. To investigate the mechanisms which underlie this, we have studied the regulation of the model genes Mdc and Il12b, whose stimulus-induced expression is tightly restricted to specific cells of the immune system. Surprisingly, we find that neither the promoter nor the enhancer sequences of these genes are sufficient to direct this cell-type specificity. Instead, the activities of upstream enh ...[more]

PMID: 22633489

Similar Datasets

Cell-type specific control of enhancer activity by H3K9 trimethylation

Project description:This SuperSeries is composed of the following subset Series: GSE32255: JmjD2d-dependence of LPS-induced genes GSE32377: Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts GSE32379: Analysis of JmjD2d-bound regions in unstimulated and stimulated dendritic cells GSE32380: Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts Refer to individual Series

2012-05-27 | E-GEOD-32381 | biostudies-arrayexpress

Analysis of JmjD2d-bound regions in unstimulated and stimulated dendritic cells

Project description:To examine JmjD2d-binding, ChIP was performed using monoclonal antibodies specific for JmjD2d, or for the JmjN domain of all JmjD2-family members. ChIP-seq for JmjD2d, Jmjd2-family, and input DNA controls, from dendritic cells under 2 conditions (unstimulated & stimulated)

2012-11-19 | E-GEOD-32379 | biostudies-arrayexpress

Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts

Project description:The distribution of H3K9me3 was analyzed in order to investigate the influence of H3K9me3 levels surrounding candidate enhancers and other cis-regulatory elements. ChIP-seq for H3K9me3 and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)

2012-11-19 | E-GEOD-32377 | biostudies-arrayexpress

Identification of candidate enhancer elements in unstimulated and stimulated dendritic cells and fibroblasts

Project description:To identify candidate enhancer elements we analyzed the distribution of two histone modifications associated with enhancers - H3K4me1 and H3K27ac - and one histone modification associated with active transcription - H4 acetylation. ChIP-seq for H3K4me1, H3K27ac and H4ac, and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)

2012-11-19 | E-GEOD-32380 | biostudies-arrayexpress

miR-155 KO in human dendritic cells

Project description:In response to inflammatory stimulation, dendritic cells (DCs) have a remarkable pattern of differentiation (maturation) that exhibits specific mechanisms to control immunity. Here, we show that in response to Lipopolysaccharides (LPS), several microRNAs (miRNAs) are regulated in human monocyte-derived dendritic cells. Among these miRNAs, miR-155 is highly up-regulated during maturation. Using LNA silencing combined to microarray technology, we have identified the Toll-like receptor / interleukin-1 (TLR/IL-1) inflammatory pathway as a general target of miR-155. We further demonstrate that miR-155 directly controls the level of important signal transduction molecules. Our observations suggest, therefore, that in mature human DCs, miR-155 is part of a negative feedback loop, which down-modulates inflammatory cytokine production in response to microbial stimuli. We devised a strategy to functionally inhibit the mature form of miR-155 with the aim of identifying the signaling pathways controlled by miR-155 during DC maturation. A LNA-modified oligonucleotide, specifically designed for miR-155 knockdown (anti-miR-155 LNA) was introduced in moDCs by nucleofection prior LPS stimulation. 24h after transfection, a reduction in miR-155 levels of 8- and 32-fold was observed by qPCR in immature and mature moDCs respectively. A comparative microarray analysis (Affymetrix U133 2.0 chip) was performed among miR-155 silenced (anti-miR-155 LNA) and control transfected (scramble LNA) moDCs, exposed or not to LPS. Thus, four samples were totally analyzed. As expected from the limited expression of miR-155 in non-activated DCs, little variation in mRNA expression (177 probe sets differentially expressed employing a cut-off of 1.5) was detected upon miR-155 silencing. Conversely, in LPS-activated cells many mRNAs (1324 probe sets, 770 up-regulated and 554 down-regulated) were affected by miR-155 inhibition.

2009-03-04 | E-GEOD-13296 | biostudies-arrayexpress

miRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation

Project description:miRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation. Immature, 4h and 16h LPS-activated moDCs were used. In this study were analysed 2 biological samples of RNA extracted from 4h-post LPS stimulation moDCs and 2 bfrom 16h-post LPS stimulation. The RNA from 0h-post LPS stimulation were used as reference sample. Were also performed dye-swaps of each biological sample as technical replicates.

2010-05-15 | E-GEOD-13369 | biostudies-arrayexpress

Gene expression analysis of dendritic cells treated with small chemical compounds

Project description:Identification of newer compounds to modulate dendritic cell functions. Total RNA obtained from bone marrow-derived dendritic cells treated for 6 hours with small chemical compounds or vehicle alone in the presence or absence of lipopolysaccharide (LPS).

2011-09-18 | E-GEOD-15360 | biostudies-arrayexpress

LPS & ATP Stimulated wild type and miR-155 KO murine C57BL/6 Dendritic Cells

Project description:Dendritic cells isolated from murine bone marrow were cultured for 7 days and then stimulated with 50 ng/mL LPS and 5 mM ATP. Cells derived from both wild type and microRNA-155 knock-out mice. Total RNA was isolated from the cells following stimulation.

2015-07-30 | E-MTAB-2608 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of dendritic cell Transcriptomes during LPS response

Project description:Purpose:The purpose of this study is to detect activated or silenced genes during LPS-induced dendritic cell. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods:Mouse dendritic cells were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse GM-CSF and IL-4, immature DCs were obtained before or after LPS stimulation. Immature DCs were sorted respectively based on marker CD86 and Iab(MHCII) using flowcytrometer. DC mRNA profiles were generated by deep sequencing,using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation during LPS stimulation. DC mRNA profiles immature BMDCs were generated by deep sequencing

2015-09-11 | E-GEOD-69256 | biostudies-arrayexpress

Expression data from mouse dendritic cells

Project description:Dendritic cells (DCs) are pivotal for both recognition of antigens and control of an array of immune responses by recognizing microbes through distinct pattern recognition receptors (PRRs). The first microbial component to be studied in detail and known to cause septic shock is endotoxin (LPS). DCs recognize LPS via Toll-like receptor TLR-47. LPS causes many changes in the DCs, but the elicitation of cytokine production is perhaps the one with clear biologic relevance. We used microarrays to detail the global programme of gene expression underlying regulation of TLR 4 signaling and identified the upregulated and downregulated genes in response to LPS treatment in mouse dendritic cells. We use microarray to determine the conserved hematopoietic miRNAs to study their potential contribution to regulating many different immunological cellular processes and contexts. To obtain overall gene expression profile, we extracted bone marrow cells from at least 3 mice for each experiment. Purified ( 97~98% purity) mouse dendritic cells, treated with LPS or control diluent, were used for RNA extraction and hybridization on Affymetrix microarrays. To obtain overall miRNA expression profile, we extracted bone marrow cells from at least 3 mice (C57BL/6) for each experiment. Purified ( 97~98% purity for CD11C+ ) mouse dendritic cells were used for RNA extraction and hybridization on Exiqon miRCURY LNATM microRNA array.

2011-04-05 | E-GEOD-28340 | biostudies-arrayexpress

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