EXPERIMENT_TITLE: GSM3985257: HiC_RIS_2; 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_2
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_2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_RIS_2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9860999", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9860999/SRR9860999", "size": "21027558028", "date": "2019-07-30 21:03:20", "md5": "ff257c080e79d3576abf81f2135b74ee", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-12441.NoIndex.HFGLHBBXX.s_3.r_2.fq.gz", "size": "17058582068", "date": "2019-07-30 20:48:31", "md5": "2c91970726b091bf81d4c2aaa6de8a0e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-12441.NoIndex.HFGLHBBXX.s_3.r_1.fq.gz", "size": "15988640318", "date": "2019-07-30 20:55:16", "md5": "5620363bf2e4c9f1a7bd862b72a48194", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9860999.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR009/9860/SRR9860999/SRR9860999.lite.1", "size": "14649556396", "date": "2022-07-09 13:04:32", "md5": "120e36d30d8b4abed658dc3de4662c3a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]