EXPERIMENT_TITLE: GSM4417624: NCI-H1975_Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, cells were fixed with 1% formaldehyde for 10 minutes at room temperture, quenched with 0.2M Glycine for 5 minutes. Adherent cells were fixed on the tissue culture plate and removed using a cell scraper. Suspension cells were fixed in suspension. After fixation and quenching, cells were pelleted, washed 1X with DPBS, pelleted again, and frozen on dry ice. Samples were stored in -80C until further processing. For RNA, cells were harvested in Trizol according to the manufacturers instrutions. After homogenization, samples were stored at -80C until further processing. RNA was isolate using the Purelink RNA mini kit with on column Dnase I treatment. RNA integrity was evaluated using RNA tapestation. In situ Hi-C was performed accoring to Rao et al. Cell 2014 using the MboI restriction enzyme. Libraries were sequenced on the NextSeq 500 platform. Stranded mRNA-seq libraries were constructed using the Illumina stranded mRNA seq kit according to the manufacturers instructions. Libaries were sequenced on the NextSeq 500 platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Higher order chromatin structure is important for regulation of genes by distal regulatory sequences. Structural variants that alter 3D genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer. However, only a small minority of structural variants are associated with altered gene expression and it remains unclear why certain structural variants lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analyzing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT, and CCND1. Using CRISPR/Cas9 genome engineering to generate de novo structural variants, we show that oncogene activity can be predicted using “Activity-by-Contact” models that consider partner region chromatin contacts and enhancer activity. However, Activity-by-Contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that structural variants that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of structural variants on oncogene activation. Overall design: Analysis of Hi-C data and structural variant in 92 cancer samples and cell lines. Analysis of Hi-C and RNA-seq data in 37 engineered cell lines. Of note, 10 of the samples from the Xu et al. study were from primary human patient tumor samples and are available through dbGap accession phs003227.
SAMPLE_TITLE: NCI-H1975_Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NCI-H1975 cell line"}, {"TAG": "cell line", "VALUE": "NCI-H1975"}, {"TAG": "experiment type", "VALUE": "MboI in situ Hi-C"}, {"TAG": "condition", "VALUE": "Wild-type"}, {"TAG": "media", "VALUE": "RPMI + 10% FBS + P/S"}]
Pool_Member_@attributes_sample_title: NCI-H1975_Hi-C
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