EXPERIMENT_TITLE: GSM3304262: HiC_library_Control_replicate1; 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_Control_replicate1
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_Control_replicate1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_library_Control_replicate1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Sample1_S1_R2_001.fastq", "size": "84456461196", "date": "2020-02-21 13:34:39", "md5": "c674f36cf04e4ea95fb1421c1002c1d7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7586416.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/586/SRR7586416.sralite.1", "size": "18311741605", "date": "2020-06-14 19:37:32", "md5": "4bf05102e8af606b8e74665a73479070", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7586416", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7586416/SRR7586416", "size": "30661551049", "date": "2018-07-24 12:43:09", "md5": "3336166b4dcc4e0934c2292f69450918", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Sample1_S1_R1_001.fastq", "size": "84465962590", "date": "2020-02-21 06:45:58", "md5": "56763b5b130efeb3cac20cb20aaabbb1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]