EXPERIMENT_TITLE: Hi-C of human colon tumor
STUDY_DESCRIPTOR_STUDY_ABSTRACT: When diagnosing cancer, pathologists use nuclear morphology as a hallmark of tumor cells, but the topological changes linked to alterations in the shape of the nucleus were poorly understood. To uncover the molecular changes that occur in the 3D structure of cancer genomes, we integrated topological maps for colon tumors and normal colon tissues with epigenetic, transcriptional, and imaging data. We characterized tumor-associated changes in chromatin loops, topologically associated domains (TADs), and large-scale compartments. We found that chromatin loop rewiring contributes to oncogenic gene expression programs. Whereas TAD structures are largely stable, the spatial partitioning of the open and closed genome compartments is compromised in tumors and is accompanied by hypomethylation... (for more see dbGaP study page.)
SAMPLE_TITLE: Computational Biology tumor Chromosome conformation capture (HiC) sample from Colorectal of a human participant in the dbGaP study "Analysis of Epigenomes and Genome Topology in Colorectal Cancer"
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "gap_accession", "VALUE": "phs002288"}, {"TAG": "submitter handle", "VALUE": "NCI_Epigenomes_Topology_CRC"}, {"TAG": "biospecimen repository", "VALUE": "NCI_Epigenomes_Topology_CRC"}, {"TAG": "study name", "VALUE": "Analysis of Epigenomes and Genome Topology in Colorectal Cancer"}, {"TAG": "study design", "VALUE": "Case Set"}, {"TAG": "biospecimen repository sample id", "VALUE": "BRD3179_hic"}, {"TAG": "submitted sample id", "VALUE": "BRD3179_hic"}, {"TAG": "submitted subject id", "VALUE": "BRD3179"}, {"TAG": "gap_sample_id", "VALUE": "4389047"}, {"TAG": "gap_subject_id", "VALUE": "3523448"}, {"TAG": "study disease", "VALUE": "Computational Biology"}, {"TAG": "body site", "VALUE": "Colorectal"}, {"TAG": "histological type", "VALUE": "Adenocarcinoma"}, {"TAG": "analyte type", "VALUE": "Chromosome conformation capture (HiC)"}, {"TAG": "is tumor", "VALUE": "Yes"}, {"TAG": "subject is affected", "VALUE": "Yes"}, {"TAG": "gap_consent_code", "VALUE": "1"}, {"TAG": "gap_consent_short_name", "VALUE": "DS-GRR-MDS"}]
Pool_Member_@attributes_sample_title: Computational Biology tumor Chromosome conformation capture (HiC) sample from Colorectal of a human participant in the dbGaP study "Analysis of Epigenomes and Genome Topology in Colorectal Cancer"
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Computational Biology tumor Chromosome conformation capture (HiC) sample from Colorectal of a human participant in the dbGaP study "Analysis of Epigenomes and Genome Topology in Colorectal Cancer"