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Cell-type specific control of enhancer activity by H3K9 trimethylation

ABSTRACT: 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

ORGANISM(S): Mus musculus

SUBMITTER: Dominic van Essen

PROVIDER: E-GEOD-32381 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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

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

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JmjD2d-dependence of LPS-induced genes

Project description: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.

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Project description:This SuperSeries is composed of the following subset Series: GSE15718: Gene expression in dendritic cells stimulated with LPS in conditions allowing or inhibiting NFAT activation GSE15720: Apoptosis genes specifically modulated by NFAT in LPS-activated dendritic cells GSE15721: Gene expression in macropages stimulated with LPS in conditions allowing or inhibiting NFAT activation Refer to individual Series

2010-03-03 | E-GEOD-15759 | biostudies-arrayexpress

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Project description:Purpose: The purpose of this study is to identify the genome-wide binding sites for IRF4 interaction partners PU.1, BATF, and JunB in dendritic cells. These ChIP-seq data were integrated with gene expression analysis in IRF4-sufficient and -deficient BMDCs in order to assemble an IRF4 gene regulatory network. Hematopoietic bone marrow progenitors from C57BL/6 mice were differentiated with GM-CSF and IL-4 for 5 days. On day 6, BMDCs were stimulated for 6 hours with 100ng/ml LPS. Fixed chromatin was immunoprecipitated with anti-PU.1, BATF, and JunB antibodies and subjected to high-throughput sequencing. The sequencing data for the input DNA was previously submitted as GSM999807.

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2010-03-04 | E-GEOD-15718 | biostudies-arrayexpress

Sumoylation-deficient bone marrow derived dendritic cells transcriptomic analysis after LPS stimulation

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Gene expression profile of murine Bone marrow derived Dendritic cells stimulated with CD40L in absence or presence of Neural Precursor cell- conditioned medium

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