EXPERIMENT_TITLE: GSM5833189: breast cancer single cell A271; 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 A271
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 A271
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer single cell A271
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A271_R1.fastq.gz", "size": "360107563", "date": "2022-01-25 10:51:49", "md5": "bc8c1f31b034c37191a01808eb24d79c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A271_R2.fastq.gz", "size": "373707619", "date": "2022-01-25 10:51:36", "md5": "c75a4d31458003bab72785bb512753ce", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17733643", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17733643/SRR17733643", "size": "481635255", "date": "2022-01-25 10:52:08", "md5": "bab6a531399b85fac222f523bb6deaf4", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17733643.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17733/SRR17733643/SRR17733643.lite.1", "size": "317396899", "date": "2022-11-06 13:33:29", "md5": "df76514a89c2175ed4dabf6cdd853fcc", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]