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A study of the effect of OxLDL on C/EBP beta binding in human macrophages using chromatin immunoprecipitation for C/EBP beta with high throughput sequencing (ChIP-seq)

ABSTRACT: We report the C/EBP beta transcription factor binding landscape in human macrophages and oxLDL-induced foam cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE66192 | GEO | 2015/04/08

SECONDARY ACCESSION(S): PRJNA276088

REPOSITORIES: GEO

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A study of the effect of OxLDL on C/EBP beta binding in human macrophages using chromatin immunoprecipitation for C/EBP beta with high throughput sequencing (ChIP-seq)

Project description:We report the C/EBP beta transcription factor binding landscape in human macrophages and oxLDL-induced foam cells ChIP-seq for C/EBP beta binding was performed in human macrophages and oxLDL induced-foam cells with quadruple biological replicates

2015-04-08 | E-GEOD-66192 | biostudies-arrayexpress

Transcriptional study of oxLDL-induced foam cell formation in WT and Atf3-/- murine bone marrow macrophages

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 experiment, we studied the effect of genetic knockout of ATF3 on the transcriptional response of macrophages to oxLDL. Murine bone marrow-derived macrophages from two different mouse strains (Atf3-/- and WT) were incubated in the presence or absence of oxidized low-density lipoprotein (oxLDL), and then transcriptionally profiled using the Affymetrix Mouse Exon Array 1.0 ST. The goal was to study the pattern of differential expression between WT and Atf3-/- strains, in oxLDL-induced foam cells and in non-foamy control cells, to identify cellular pathways that may be dysregulated under loss of the transcription factor ATF3 in macrophage foam cells.

2012-03-23 | GSE32358 | GEO

Transcriptional study of oxLDL-induced foam cell formation in WT and Atf3-/- murine bone marrow macrophages

2012-03-23 | E-GEOD-32358 | biostudies-arrayexpress

Transcriptome profiling of responses of mouse peritoneal macrophages to oxLDL

Project description:The goal of this study was to profile transcriptional changes of mouse peritoneal macrophages during foam cell formation induced by the atherogenic lipoprotein, oxidized LDL (oxLDL)

2014-12-04 | GSE58913 | GEO

human primary monocytes: Control vs. oxLDL(oxidized low density lipoprotein)-stimulated 6h vs oxLDL-stimulated 12h

Project description:total RNA profiling of human primary monocytes comparing control untreated oxLDL cells with oxLDL cells for different time (6h and 12h), The latter makes monocytes to macrophage and foam cells.

2009-04-03 | GSE15514 | GEO

Chromatin immunoprecipitation with next generation sequencing (ChIP-seq) of H3K27ac in primary human macrophages and foam cells

Project description:We report the enhancer landscape in primary human macrophages and foam cells using ChIP-seq for the H3K27ac histone mark CD14+ monocytes were isolated from the blood of 2 healthy male volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting 4 samples were then subjected to ChIP-seq for H3K27ac.

2015-04-08 | E-GEOD-54972 | biostudies-arrayexpress

Arraystar circRNA array data for foam cells formation in phorbol 12-myristate 13-acetate-induced macrophages model

Project description:The phagocytosis of oxidized low-density lipoprotein (oxLDL) by monocyte-derived macrophages and the subsequent differentiation of macrophages into foam cells are the key steps in atherogenesis. Our study provides a potential new therapeutic strategy to alleviate oxLDL accumulation and foam cell formation.

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Gene expression in primary human macrophages and foam cells

Project description:The aim of the experiment was to determine the effects of 48 hours of treatment with oxidized low density lipoprotein (oxLDL) on gene expression in primary human monocyte-derived macrophages. 6 independent biological replicates were processed. From each replicate half of the cells were treated with oxLDL and the other half were treated with the control buffer. For foam cell formation (after 7 days) macrophages were treated with oxLDL (50mcg/ml, enodtoxin free, Copper oxidized). Control macrophages were treated with a matching buffer without oxLDL. Treatment duration - 48 hours.

2015-04-08 | E-GEOD-54666 | biostudies-arrayexpress

monocyte reprogramming by oxLDL

Project description:We have performed analyses of murine primary bone marrow derived monocytes challenged with either PBS or oxLDL. oxLDL selectively enhances growth and adhesion potential of monocytes. Purified bone marrow monocytes were treated with PBS or 20 microgram/ml oxLDL for a five day period, and cells were harvested for scRNAseq analyses.

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Formaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) in primary human macrophages and foam cells

Project description:We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting six samples were then subjected to FAIRE-seq using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).

2015-04-08 | E-GEOD-54971 | biostudies-arrayexpress

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