EXPERIMENT_TITLE: GSM5851260: breast cancer MCF7TR 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 MCF7TR replicate 1 [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MCF7TR"}, {"TAG": "cell types", "VALUE": "immortalized breast epithelial cell"}, {"TAG": "cell line", "VALUE": "MCF7TR"}, {"TAG": "analysis", "VALUE": "Hi-C"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: breast cancer MCF7TR replicate 1 [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: breast cancer MCF7TR replicate 1 [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF7TR_Rep1_R1.fastq.gz", "size": "5569856251", "date": "2022-01-31 15:12:11", "md5": "d5c404f63f80c9e2f3605e4dc5625f20", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MCF7TR_Rep1_R2.fastq.gz", "size": "6673915864", "date": "2022-01-31 15:14:57", "md5": "24db0bf2b1d44b55310497406382fe70", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17836752", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17836752/SRR17836752", "size": "7377910672", "date": "2022-01-31 15:19:35", "md5": "595b56aa6d077882c84cb31f3afbd63a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17836752.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR017/17836/SRR17836752/SRR17836752.lite.1", "size": "4009658576", "date": "2022-11-06 13:55:30", "md5": "3c222fe7e09450de36ac42cef4da4e04", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]