EXPERIMENT_TITLE: GSM4072701: 16-178.Normal; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Patient tissue sample was pulverized by repeated hammering while frozen in liquid nitrogen to produce tissue powder. For in-situ Hi-C, tissue was crosslinked, lysed and disgested with MboI. The fragments were the labelled with biotin, proximally ligated, sonicated, and purified with AMPure XP beads. Ligated DNA was pulled down with streptavidin T1 beads, followed by manual library preparation. In situ Hi-C library was sequenced with Illumina Hiseq4000 and Novaseq S4 platforms.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed. Overall design: This study contains in situ Hi-C data for colorectal cancer patient samples. Additional processed data is available at: http://junglab.kaist.ac.kr/Dataset/Kim_et_al_2023 Online tissue slide data repository is available at: http://junglab.kaist.ac.kr/Dataset/CellReports_tissueData.html
SAMPLE_TITLE: 16-178.Normal
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "16-178"}, {"TAG": "experiment", "VALUE": "in situ Hi-C"}, {"TAG": "disease", "VALUE": "Normal"}]
Pool_Member_@attributes_sample_title: 16-178.Normal
RUN_SET_RUN_Pool_Member_@attributes_sample_title: 16-178.Normal
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