EXPERIMENT_TITLE: GSM4908719: LNCaP-M1E10; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: ARIMA's Hi-C kit (ARIMA Genomics) were applied for capturing proximally-ligated DNA. The biotinylated DNA was sheared to a size of 300–500 bp. Libraries were constructed following Kapa Hyper Prep Kit (KAPA) protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Recent efforts have shown that structural variations (SVs) can disrupt three-dimensional genome organization and induce enhancer hijacking, yet no computational tools exist to identify such events from chromatin interaction data. Here, we develop NeoLoopFinder, a computational framework to identify the chromatin interactions induced by SVs, including interchromosomal translocations, large deletions and inversions. Our framework can automatically resolve complex SVs, reconstruct local Hi-C maps surrounding the breakpoints, normalize copy number variation and allele effects and predict chromatin loops induced by SVs. We applied NeoLoopFinder in Hi-C data from 50 cancer cell lines and primary tumors and identified tens of recurrent genes associated with enhancer hijacking. To experimentally validate NeoLoopFinder, we deleted the hijacked enhancers in prostate adenocarcinoma cells using CRISPR–Cas9, which significantly reduced expression of the target oncogene. In summary, NeoLoopFinder enables identification of critical oncogenic regulatory elements that can potentially reveal therapeutic targets. Overall design: In situ Hi-C was used to probe the chromatin interaction changes after deleting the hijacked enhancers in LNCaP cells. 4C-Seq was used to probe the chromatin interaction anchored at MYC gene in SKNMC cells
SAMPLE_TITLE: LNCaP-M1E10
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "prostate cancer metastatic site"}, {"TAG": "cell type", "VALUE": "LNCaP cells"}, {"TAG": "assay", "VALUE": "Hi-C"}]
Pool_Member_@attributes_sample_title: LNCaP-M1E10
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LNCaP-M1E10
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