EXPERIMENT_TITLE: GSM3399745: SW480_HiC-Rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed using the in situ Hi-C protocol as previously described in Rao et al., 2014, using 2-5 million cells per experiment digested with the MboI restriction enzyme. The libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq LT adaptors.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Genomic material within the nucleus is folded into successive layers in order to package and organize the long string of linear DNA. This hierarchical level of folding is closely associated with transcriptional regulation and DNA replication. Genes within the same folding domain demonstrate similar expression and histone-modification profiles1. Therefore, boundaries separating different domains have important roles in reinforcing the stability of these domain-wide features. Indeed, domain boundary disruptions in human genetic disorders2,3 or human cancers lead to misregulation of certain genes4,5, due to de novo enhancer exposure to promoters. However, the frequency of boundary disruptions in human cancers, and whether there are recurrently affected boundaries in specific cancer types, remains unclear. Here, to understand effects and distributions of somatic structural variations (SVs) across TADs, we utilized 288,457 high-confidence somatic structural variations from 2658 high-coverage whole genome sequencing datasets across various cancer types. We comprehensively profiled structural variations effects on the domain boundaries and the regulation of genes in human cancers. Notably, most of the TAD disruptions do not result in appreciable changes in nearby gene expression where more than 2-fold expression change was observed in only 14% of regions with the boundary deletions. In addition, we demonstrated that SV types affect TADs differently, specifically, complex rearrangements drastically change chromatin folding maps in the cancer genomes. Overall design: Profiling chromatin conformation dynamics in four cancer cell lines.
SAMPLE_TITLE: SW480_HiC-Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "SW480_HiC"}, {"TAG": "cell line", "VALUE": "SW480"}, {"TAG": "cell type", "VALUE": "Colon cancer cell line"}]
Pool_Member_@attributes_sample_title: SW480_HiC-Rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: SW480_HiC-Rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7896721.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR007/896/SRR7896721.sralite.1", "size": "4440000549", "date": "2020-06-20 13:30:39", "md5": "449cfa9c022848a401b9dc285aa2a782", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7896721", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7896721/SRR7896721", "size": "10354574285", "date": "2018-09-24 22:08:01", "md5": "8b7b746c788915878d837d99d5080bda", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SW480-Rep1_R2.fastq.gz", "size": "7268180262", "date": "2020-02-13 18:11:00", "md5": "40fca31c64a3d4c7f969acf61eb5b43a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SW480-Rep1_R1.fastq.gz", "size": "7233665592", "date": "2020-02-13 13:43:31", "md5": "da8f48949886e8c00dbaa171b4825155", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]