EXPERIMENT_TITLE: GSM3985254: HiC_Growing_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_Growing_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": "No"}]
Pool_Member_@attributes_sample_title: HiC_Growing_2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_Growing_2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9860995.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/9860/SRR9860995/SRR9860995.lite.1", "size": "17366207141", "date": "2022-07-21 14:28:58", "md5": "1a8571d81227c54593580b24b722ab49", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9860995", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9860995/SRR9860995", "size": "33034492085", "date": "2019-07-30 20:47:28", "md5": "fb1423120fb1ced716b53d7eab3bf026", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10243.NoIndex.C8B9UANXX.s_1.r_2.fq.gz", "size": "24012763739", "date": "2019-07-30 20:11:30", "md5": "366188aa3b29baa9e16e0d7ad88e3a9c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10243.NoIndex.C8B9UANXX.s_1.r_1.fq.gz", "size": "24321112285", "date": "2019-07-30 20:00:47", "md5": "b57ddb65aeab52aa975f4741c830c524", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]