EXPERIMENT_TITLE: GSM3985253: HiC_Growing_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_Growing_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": "No"}]
Pool_Member_@attributes_sample_title: HiC_Growing_1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR9860993", "SUBMITTER_ID": "GSM3985253_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187716", "EXTERNAL_ID": ["SAMN12414277", "GSM3985253"]}, "@attributes": {"member_name": "", "accession": "SRS5187716", "sample_name": "GSM3985253", "sample_title": "HiC_Growing_1", "spots": "224809133", "bases": "33721369950", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9860993.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR009/9860/SRR9860993/SRR9860993.lite.1", "size": "8857113468", "date": "2022-07-09 13:05:35", "md5": "f73020bfcca9656e5985c3327bebf449", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9860993", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9860993/SRR9860993", "size": "21357786901", "date": "2019-07-30 19:49:01", "md5": "2a3ca3d417fb813cc4e2382b1672970a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10241.NoIndex.C80L9ANXX.s_7.r_2.fq.gz", "size": "15344476607", "date": "2019-07-30 19:22:50", "md5": "3c0835ada26a8bd43314ed9db8720f7b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10241.NoIndex.C80L9ANXX.s_7.r_1.fq.gz", "size": "15528481613", "date": "2019-07-30 19:30:12", "md5": "99fdb5161ccaf993d25da8d835540fa7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "224809133"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "33721369950"}}, "@attributes": {"alias": "GSM3985253_r1", "accession": "SRR9860993", "total_spots": "224809133", "total_bases": "33721369950", "size": "21357785150", "load_done": "true", "published": "2020-10-06 16:14:05", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR9860994", "SUBMITTER_ID": "GSM3985253_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187716", "EXTERNAL_ID": ["SAMN12414277", "GSM3985253"]}, "@attributes": {"member_name": "", "accession": "SRS5187716", "sample_name": "GSM3985253", "sample_title": "HiC_Growing_1", "spots": "239732218", "bases": "35959832700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9860994", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9860994/SRR9860994", "size": "17666053078", "date": "2019-07-30 19:24:20", "md5": "079f44ff47a7e2e6ddc07e95b34141ce", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10241.NoIndex.C81WJANXX.s_7.r_2.fq.gz", "size": "13330565336", "date": "2019-07-30 19:12:19", "md5": "349b6625d45c9689926d9c54bdd1397c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10241.NoIndex.C81WJANXX.s_7.r_1.fq.gz", "size": "14236740910", "date": "2019-07-30 19:15:18", "md5": "05c8c2a85f15c744a91afe9d060f297c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9860994.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/9860/SRR9860994/SRR9860994.lite.1", "size": "9395370062", "date": "2022-07-21 14:43:04", "md5": "abe0751d3b9f0f755fcc5a35fdc6eb11", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "239732218"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "35959832700"}}, "@attributes": {"alias": "GSM3985253_r2", "accession": "SRR9860994", "total_spots": "239732218", "total_bases": "35959832700", "size": "17666051325", "load_done": "true", "published": "2020-10-06 16:14:05", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]