EXPERIMENT_TITLE: GSM3985258: cHiC_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: cHiC_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: cHiC_Growing_1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR9861000", "SUBMITTER_ID": "GSM3985258_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187720", "EXTERNAL_ID": ["SAMN12414272", "GSM3985258"]}, "@attributes": {"member_name": "", "accession": "SRS5187720", "sample_name": "GSM3985258", "sample_title": "cHiC_Growing_1", "spots": "248816200", "bases": "24881620000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9861000", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9861000/SRR9861000", "size": "11900567905", "date": "2019-07-30 19:24:25", "md5": "9a2fff4dd3ca8be48e67225e7ce1bc34", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9861000.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR009/9861/SRR9861000/SRR9861000.lite.1", "size": "6631092237", "date": "2022-07-21 14:02:38", "md5": "0f860733ddb86136aadb206e9778cc2f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E12ANXX.s_1.r_2.fq.gz", "size": "10327676829", "date": "2019-07-30 19:10:43", "md5": "c279b725f203c760fa57134b6ad65904", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E12ANXX.s_1.r_1.fq.gz", "size": "9617821778", "date": "2019-07-30 19:15:00", "md5": "9d1ad87dd2d18fababa41e869c2a503e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "248816200"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "24881620000"}}, "@attributes": {"alias": "GSM3985258_r1", "accession": "SRR9861000", "total_spots": "248816200", "total_bases": "24881620000", "size": "11900566156", "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": "SRR9861001", "SUBMITTER_ID": "GSM3985258_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187720", "EXTERNAL_ID": ["SAMN12414272", "GSM3985258"]}, "@attributes": {"member_name": "", "accession": "SRS5187720", "sample_name": "GSM3985258", "sample_title": "cHiC_Growing_1", "spots": "246753704", "bases": "24675370400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9861001.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/9861/SRR9861001/SRR9861001.lite.1", "size": "6575712943", "date": "2022-07-05 22:43:24", "md5": "c0763039b6cf55b9768f319c94a57534", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9861001", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9861001/SRR9861001", "size": "11813695243", "date": "2019-07-30 19:26:22", "md5": "84a83219cdbdb0634ed76fd1e44ea165", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E12ANXX.s_2.r_2.fq.gz", "size": "10189068138", "date": "2019-07-30 19:08:27", "md5": "f70b68ae18b78afeb7c76f6f7c9ccbc2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E12ANXX.s_2.r_1.fq.gz", "size": "9613060052", "date": "2019-07-30 19:16:11", "md5": "60438b3d15800f8c7e73be3baeb32a21", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "246753704"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "24675370400"}}, "@attributes": {"alias": "GSM3985258_r2", "accession": "SRR9861001", "total_spots": "246753704", "total_bases": "24675370400", "size": "11813693497", "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": "SRR9861002", "SUBMITTER_ID": "GSM3985258_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187720", "EXTERNAL_ID": ["SAMN12414272", "GSM3985258"]}, "@attributes": {"member_name": "", "accession": "SRS5187720", "sample_name": "GSM3985258", "sample_title": "cHiC_Growing_1", "spots": "250040156", "bases": "37506023400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9861002.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/9861/SRR9861002/SRR9861002.lite.1", "size": "9836365165", "date": "2022-07-05 22:50:13", "md5": "9efa41d0744dc4fabd53ad709386ee01", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9861002", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9861002/SRR9861002", "size": "22466072295", "date": "2019-07-30 19:46:39", "md5": "e0a347cebceef56d58327b42fa253b4e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E5UANXX.s_1.r_2.fq.gz", "size": "18232208588", "date": "2019-07-30 19:34:27", "md5": "8fcfba6e67b34a812e2d62a30f297c6a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E5UANXX.s_1.r_1.fq.gz", "size": "14136687443", "date": "2019-07-30 19:26:11", "md5": "2a691126dd32e43e4ea12a936ae31457", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "250040156"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "37506023400"}}, "@attributes": {"alias": "GSM3985258_r3", "accession": "SRR9861002", "total_spots": "250040156", "total_bases": "37506023400", "size": "22466070545", "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": "SRR9861003", "SUBMITTER_ID": "GSM3985258_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS5187720", "EXTERNAL_ID": ["SAMN12414272", "GSM3985258"]}, "@attributes": {"member_name": "", "accession": "SRS5187720", "sample_name": "GSM3985258", "sample_title": "cHiC_Growing_1", "spots": "238936814", "bases": "35840522100", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9861003.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/9861/SRR9861003/SRR9861003.lite.1", "size": "9401744041", "date": "2022-07-05 23:07:26", "md5": "026321f9ce9bc7350c12b1956b101d3a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9861003", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9861003/SRR9861003", "size": "21933293899", "date": "2019-07-30 20:02:00", "md5": "56f60c481f42862f63ef3002a2cafad1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E5UANXX.s_2.r_2.fq.gz", "size": "17339800240", "date": "2019-07-30 19:45:29", "md5": "cb0578a6f180f5415fd98982df19544f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SLX-10245.NoIndex.C8E5UANXX.s_2.r_1.fq.gz", "size": "14002705919", "date": "2019-07-30 19:38:05", "md5": "78ab0e831bf9b766a069384035ca616c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "238936814"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "35840522100"}}, "@attributes": {"alias": "GSM3985258_r4", "accession": "SRR9861003", "total_spots": "238936814", "total_bases": "35840522100", "size": "21933292149", "load_done": "true", "published": "2020-10-06 16:14:05", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]