EXPERIMENT_TITLE: GSM3682157: ZR75-1 parental; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Extraction of cell nucleus and DNA were performed as described (Rao et al. 2014). In situ Hi-C was performed as described (Rao et al. 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We developed a novel computational model, HiSIF (Hi-C Significant Interacting Fragments), which uses a Poisson Mixture Model (PMM) with a power-law decay background. We compared its performance to some existing programs with publicly available Hi-C data, and then applied it to in situ Hi-C data in breast cancer sensitive and resistant cells. Overall design: In this study, we tested the model in our newly generated Hi-C data in three ERa positive breast cancer cell lines, MCF7, tamoxifen-resistant MCF7 (MCF7-TamR) (MCF7 and MCF7-TamR data have been deposited in GEO under accession number GSE108787), T47D and tamoxifen-resistant T47D (T47D-TamR), ZR75-1 and tamoxifen-resistant ZR75-1 (ZR75-1-TamR).
SAMPLE_TITLE: ZR75-1 parental
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "ZR75-1"}, {"TAG": "cell line background", "VALUE": "ZR75-1"}, {"TAG": "cell type", "VALUE": "immortalized breast epithelial cell line"}, {"TAG": "phenotype", "VALUE": "control; parental"}, {"TAG": "analysis", "VALUE": "in situ Hi-C"}]
Pool_Member_@attributes_sample_title: ZR75-1 parental
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