EXPERIMENT_TITLE: GSM5833144: breast cancer single cell A226; 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 A226
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF7TR"}, {"TAG": "cell line", "VALUE": "MCF7TR"}, {"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 A226
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer single cell A226
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17733736.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17733/SRR17733736/SRR17733736.lite.1", "size": "446941510", "date": "2022-10-16 12:50:32", "md5": "828e47778f16120221ac7bd17c6effe1", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17733736", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17733736/SRR17733736", "size": "843453462", "date": "2022-01-25 10:52:26", "md5": "c51b7e1dfd9dfcc2c00cbb661f688755", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A226_R2.fastq.gz", "size": "555036490", "date": "2022-01-25 10:51:54", "md5": "a14b84b28fc64ec04d4963df571592b2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A226_R1.fastq.gz", "size": "754644695", "date": "2022-01-25 10:51:23", "md5": "ae4f68d368a13a96740986d85c436fb9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]