EXPERIMENT_TITLE: GSM5833110: breast cancer single cell A192; 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 A192
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 A192
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer single cell A192
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A192_R1.fastq.gz", "size": "3043911311", "date": "2022-01-25 11:50:09", "md5": "5df3f417db567a8ed17e5e44875e2627", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A192_R2.fastq.gz", "size": "2977019129", "date": "2022-01-25 11:48:34", "md5": "589bd47bfd84b1449d8f1041e65930a7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17733746", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17733746/SRR17733746", "size": "5126011128", "date": "2022-01-25 11:55:08", "md5": "962ccc77159a9b255be0afcdc09383c8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17733746.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17733/SRR17733746/SRR17733746.lite.1", "size": "3029824888", "date": "2022-10-17 17:10:11", "md5": "0982517f775b1839a21be808df41b13e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]