EXPERIMENT_TITLE: GSM5851258: breast cancer MCF7M1 replicate 1 [Hi-C]; 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). Hi-C was performed as described (Rao et al. 2014).
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. Population cells Hi-C data as the reference. 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. Population cells Hi-C data as the reference. This is the dataset stored for population cells.
SAMPLE_TITLE: breast cancer MCF7M1 replicate 1 [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF7M1"}, {"TAG": "cell types", "VALUE": "immortalized breast epithelial cell"}, {"TAG": "cell line", "VALUE": "MCF7M1"}, {"TAG": "analysis", "VALUE": "Hi-C"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: breast cancer MCF7M1 replicate 1 [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer MCF7M1 replicate 1 [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF7M1_Rep1_R1.fastq.gz", "size": "11550730309", "date": "2022-01-31 20:03:46", "md5": "daa373763fc28fc456050362348e65d7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF7M1_Rep1_R2.fastq.gz", "size": "12998539550", "date": "2022-01-31 20:16:06", "md5": "9763de4caa83e0cc8d4061e8e6abe3ab", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17836754", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17836754/SRR17836754", "size": "14960283967", "date": "2022-01-31 20:36:04", "md5": "5a7312b52d84a3dc3e562166bed97959", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17836754.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17836/SRR17836754/SRR17836754.lite.1", "size": "8973862667", "date": "2022-11-01 03:18:50", "md5": "84125b96b9563d0c90e685e2de6d0bf5", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]