EXPERIMENT_TITLE: GSM3985256: HiC_RIS_1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was carried out according to the in-nucleus ligation protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175). Capture Hi-C was carried out with SureSelect target enrichment (Agilent Technologies), using a custom-designed biotinylated RNA bait library targetting regions of interest in the human genome and custom paired-end blockers according to the manufacturer's instructions (Agilent Technologies).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Senescence is a stable form of cell cycle arrest that is triggered in response to various pathophysiological stimuli. The three-dimensional structure of senescent cells has been previously characterised, mostly in terms of macro-domains or changes between large heterochromatic regions. In the present body of work, using a combination of HiC and targetted Capture Hi-C, we aimed to investigate the association between gene expression and local chromatin structure in senescence, particularly focusing on enhancer-promoter (EP) interactions. We show that many EP contacts are rewired in RAS-induced Senescence compared to 'normal', growing cells and that these are associated with cohesin binding changes and possible loop re-organisation. The genes affected by altered chromatin interactions correspond to the two main axes of senescence gene regulation: cell cycle and inflammation. Our findings are potentially relevant during ageing and in cancers with cohesin mutations, where cell cycle and inflammation are also deregulated. Overall design: HiC and Capture HiC of growing and (RAS-induced) senescent IMR90 fibroblasts
SAMPLE_TITLE: HiC_RIS_1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "IMR90"}, {"TAG": "cell line", "VALUE": "IMR90"}, {"TAG": "passage", "VALUE": "20-25"}, {"TAG": "vector", "VALUE": "ER:HRAS(G12V)"}, {"TAG": "tamoxifen", "VALUE": "Yes, 6 days"}]
Pool_Member_@attributes_sample_title: HiC_RIS_1
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