EXPERIMENT_TITLE: GSM7445526: HI-C DIvA_mock; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: gDNA extraction,Qiagen PureGene Libraries were contructed using Indel-seq and Hi-C protocol
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay (Indel-Seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentallyinduced and spontaneous genome instability. Templated insertions, which derive from sequences genome-wide, require contact between donor and acceptor loci, homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-Seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop followed by DNA synthesis, displacement and then ligation by nonhomologous end-joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that are distinct from cut-and-paste events Overall design: Indel-seq, Hi-C
SAMPLE_TITLE: HI-C DIvA_mock
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "U2OS"}, {"TAG": "cell type", "VALUE": "Cancer Cell line"}, {"TAG": "cell line", "VALUE": "U2OS"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "treatment", "VALUE": "mock/DMSO"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: HI-C DIvA_mock
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