EXPERIMENT_TITLE: GSM3304265: HIC_library_CBL0137-treated_replicate2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed in two biological replicates using the DpnII restriction endonuclease according to a previously published protocol(Lieberman-Aiden Et al. 2009 (PMID: 19815776);Belton Et al. 2012(PMID: 22652625 )).Each Hi-C library was sequenced using paired end sequencing on an Illumina HiSeq 3000 in two technical replicates;
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We have recently discovered a class of anti-cancer agents, curaxins, which suppress transcription of oncogenes. Here we demonstrate that curaxins preferentially downregulate expression of genes controlled by enhancers and super-enhancers via interrupting enhancer/promoter spatial communication. Our observations made both on a model of enhancer-regulated transcription of chromatinized template and on cultured cancer cells allow classifying curaxins as a novel type of epigenetic drugs that target the 3D genome organization. Overall design: Processed and raw HiC data for control and CBL0137-treated HT1080 cells.
SAMPLE_TITLE: HIC_library_CBL0137-treated_replicate2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "connective tissue"}, {"TAG": "tissue", "VALUE": "HT1080 cells"}, {"TAG": "disease", "VALUE": "fibrosarcoma"}, {"TAG": "oncogene", "VALUE": "ras +"}]
Pool_Member_@attributes_sample_title: HIC_library_CBL0137-treated_replicate2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HIC_library_CBL0137-treated_replicate2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7586419", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7586419/SRR7586419", "size": "27121716503", "date": "2018-07-24 12:22:00", "md5": "5eb41de14fad814c4a8ba3d43eb6e62d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Sample4_S4_R2_001.fastq", "size": "78386158766", "date": "2020-02-21 06:43:31", "md5": "9c38b7e355145cf6b83a885cd7099fb0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Sample4_S4_R1_001.fastq", "size": "78406353672", "date": "2020-02-21 13:34:39", "md5": "035bf0d33b70b167255c75ee10d97f3b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7586419.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/586/SRR7586419.sralite.1", "size": "16997325595", "date": "2021-06-15 21:12:40", "md5": "ed61e900d1ab3b16916ce98a2e832f69", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]