EXPERIMENT_TITLE: GSM5833176: breast cancer single cell A258; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Extraction of cell nucleus and DNA were performed as described (Flyamer et al. 2017, doi:10.1038/nature21711). single-cell Hi-C was performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Anticancer drug therapy generally elicits the drug tolerance after long-term treatment. Recent studies suggested that 3D chromatin structures of cancer cells were intimately linked to drug resistance. However, 3D chromatin structures in drug-tolerant cancer cells at single-cell resolution haven't been elucidated. Here we performed single-cell Hi-C (scHi-C) analysis to examine the 3D chromatin structures in three stages of breast cancer cells. Overall design: To fully understand the 3D chromatin structures of drug-tolerant cancer cells at single-cell resolution, we designed scHi-C approach for analyzing a breast cancer cell model system, MCF7, MCF7M1 and MCF7TR cells. A total of 293 cells (89 MCF7 cells, 91 MCF7M1 cells, 113 MCF7TR cells) were used for scHi-C profiling.
SAMPLE_TITLE: breast cancer single cell A258
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF7M1"}, {"TAG": "cell line", "VALUE": "MCF7M1"}, {"TAG": "cell type", "VALUE": "immortalized breast epithelial cell line"}, {"TAG": "treatment", "VALUE": "untreated"}, {"TAG": "analysis", "VALUE": "single-cell Hi-C"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: breast cancer single cell A258
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer single cell A258
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A258_R1.fastq.gz", "size": "183940667", "date": "2022-01-25 10:46:10", "md5": "20c01b9a1107d7797b56c2a3ca4d4db4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A258_R2.fastq.gz", "size": "191487464", "date": "2022-01-25 10:46:04", "md5": "00b587d836ed877b29c1c56c7c2d7a55", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17733680", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17733680/SRR17733680", "size": "267630849", "date": "2022-01-25 10:46:23", "md5": "6b856c82982c9f61579ae6b7cd2c377b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17733680.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17733/SRR17733680/SRR17733680.lite.1", "size": "173339329", "date": "2022-10-18 07:31:34", "md5": "57f2e3cfdfe692d39530ec174624250e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]