GSE137188
3D chromatin structure in colon cancer
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