EXPERIMENT_TITLE: Illumina HiSeq 2500 paired end sequencing
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Targeted capture Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression. We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 ndependent breast cancer risk signals, and explore the functional mechanism underlying altered risk at the 12q24 risk region. Our results demonstrate the power of combining genetics, computational genomics and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.
SAMPLE_TITLE: MCF10A human non-tumourigenic mammary epithelial cells
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA-FIRST-PUBLIC", "VALUE": "2019-01-14T17:03:32Z"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2018-11-15T00:40:04Z"}, {"TAG": "External Id", "VALUE": "SAMEA5089560"}, {"TAG": "INSDC center name", "VALUE": "QIMR BERGHOFER"}, {"TAG": "INSDC first public", "VALUE": "2019-01-14T17:03:32Z"}, {"TAG": "INSDC last update", "VALUE": "2018-11-15T00:40:04Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "MCF10A"}, {"TAG": "cell type", "VALUE": "mammary epithelial cell"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "sample name", "VALUE": "MCF10A"}, {"TAG": "scientific_name", "VALUE": "Homo sapiens"}, {"TAG": "tissue type", "VALUE": "breast"}]
Pool_Member_@attributes_sample_title: MCF10A human non-tumourigenic mammary epithelial cells
RUN_SET_RUN_Pool_Member_@attributes_sample_title: MCF10A human non-tumourigenic mammary epithelial cells
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