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ChRO-seq on TeloHAEC cells before and after TNFα stimulation

ABSTRACT: ChRO-seq on TeloHAEC cells before and after TNFα stimulation

PROVIDER: PRJEB39796 | ENA |

REPOSITORIES: ENA

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ChRO-seq on TeloHAEC cells before and after TNFα stimulation

Project description:We performed chromatin run on and sequencing (ChRO-seq) on TeloHAEC cells before and after TNFα stimulation to map locations of RNA polymerase and quantify nascent transcription at RELA peaks.

2020-08-20 | E-MTAB-9425 | biostudies-arrayexpress

RNA-seq of primary aortic human endothelial cells before and after TNFα stimulation

Project description:To characterize the transcriptome of primary vascular endothelial cells (ECs) during TNFα-response, we performed total RNA-seq on primary human aortic ECs (HAEC), before and after TNFα (45 min. 10 ng/mL).

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Multi-species RELA ChIP-seq of mammalian aortic endothelial cells before and after TNFα stimulation

Project description:TNFα has an evolutionary conserved role in mediating inflammation via activation of the transcription factor NF-κB. The functions of individual NF-κB binding sites are not well understood. To identify conserved and functionally important NF-κB binding sites in mammals, we performed ChIP-seq to map the genome-wide binding of RELA and select histone modifications in primary vascular endothelial cells (ECs) isolated from the aortas of human (HAEC), mouse (MAEC) and cow (BAEC), before and after TNFα. The conserved RELA binding sites show strong epigenetic changes in response to TNFα and enrich near genes controlling vascular development and pro-inflammatory responses. Our method identifies novel modes of RELA-chromatin interactions that are conserved in mammals and shared between multiple cell-types. Particularly, genomic regions bound by RELA prior to stimulation are important responders during TNFα stimulation. We use CRISPR/Cas9 genome editing to validate the roles of the conserved RELA pre-bound sites near pro-inflammatory genes such as CCL2 and PLK2. Our evolutionary approach describes new aspects of mammalian NF-κB biology including its role within super-enhancers and relevance in inflammatory disorders.

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RNA-seq of primary aortic human endothelial cells before and after TNFα stimulation

Project description:RNA-seq of primary aortic human endothelial cells before and after TNFα stimulation

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ATAC-seq of primary mammalian aortic endothelial cells before and after TNFα stimulation

Project description:ATAC-seq of primary mammalian aortic endothelial cells before and after TNFα stimulation

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ATAC-seq of primary mammalian aortic endothelial cells before and after TNFα stimulation

Project description:To identify conserved TNFα-induced changes in chromatin-accessibility in mammals, we performed ATAC-seq in primary vascular endothelial cells (ECs) isolated from the aortas of human (HAEC), mouse (MAEC) and cow (BAEC), before and after TNFα. We overlay our data with multi-species NF-κB binding data and identify multiple modes of NF-κB-chromatin interactions that are conserved during mammalian TNFα response. Our cross-species approach identifies conserved changes in chromatin-accessibility at NF-κB binding sites that are disease-relevant and essential during mammalian acute inflammation.

2020-06-01 | E-MTAB-7878 | biostudies-arrayexpress

Multi-species RELA ChIP-seq of mammalian aortic endothelial cells before and after TNFα stimulation

Project description:Multi-species RELA ChIP-seq of mammalian aortic endothelial cells before and after TNFα stimulation

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Transcriptome analysis of IEC4.1 cells in response to TNFα stimulation.

Project description:Mouse intestinal epithelial cells (IEC4.1 cells) were stimulated with TNFα (10 ng/ml) for 4h. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A). IEC4.1 cells were grown to 80% confluence for four groups: the siRNA control (Group A, cells treated with a non-specific scrambied siRNA control), the TNFα -stimulated (Group B, cells treated with the siRNA control plus TNFα stimulation), lincRNA-Cox2 siRNA (Group C, cells treated with an siRNA to lincRNA-Cox2), and lincRNA-Cox2 siRNA/ TNFα stimulated (Group D, cells treated with the lincNRA-Cox2 siRNA plus TNFα stimulation). Cells were treated with the siRNAs for 24h, followed by additional culture for 4h in the presence or absence of TNFα (10 ng/ml). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction (Ambion).

2016-10-25 | E-MTAB-3904 | biostudies-arrayexpress

Multi-species RELA, JUN, and histone modification ChIP-seq of mammalian aortic endothelial cells before and after TNFα stimulation

Project description:Multi-species RELA, JUN, and histone modification ChIP-seq of mammalian aortic endothelial cells before and after TNFα stimulation

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Genome-wide TNFα-induced p65 binding before and after telomerase inhibition in HeLa cells

Project description:Chromatin immunoprecipitation sequencing (ChIP-seq) was performed to analyze the effect of telomerase inhibition on TNFα-induced genome-wide p65 binding in HeLa cells. By obtaining over 40 million uniquely mappable reads per sample from ChIP-seq, maps for TNFα-induced p65 binding in absence and presence of an hTERT inhibitor, MST-312, were generated. As expected, TNFα treatment significantly increased genome-wide p65 occupancy. Interestingly, when cells were treated with MST-312 prior to TNFα stimulation, the number of p65 binding sites was reduced. In addition, some binding sites, including important p65 targets like IL6 and TNF, showed a reduced p65 occupancy with a minimum fold change of 1.5, after MST-312 exposure. Taken together, our ChIP-seq data indicate that telomerase is required for optimal p65 binding at a small proportion of p65 target sites upon inflammatory stimuli.

2012-11-26 | GSE41100 | GEO

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