EXPERIMENT_TITLE: GSM5098080: Hi-C_TNBC_Tissue8; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: (Hi-C) The in situ Hi-C experiments for cells and tissues was performed according to the Arima-HiC protocol (Arima Genomics, Inc.; Cat #A160259). (Hi-C) The Hi-C library was generated using the Arima-HiC kit (Arima Genomics, Inc.; Cat #A510008)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Triple-negative breast cancer (TNBC) is malignant cancer with a high risk of recurrence. To date, the underlying 3D chromatin organizations of TNBC have remained unclear. Here, using in situ Hi-C, we characterized the 3D chromatin organizations in cells representing five distinct subtypes of breast cancer (including TNBC) and TNBC tissues, compared to normal cells/tissues. We found that the global and local 3D architectures are severely disrupted in TNBC cells. Importantly, we detected CTCF-dependent TNBC-susceptible loss/gain of 3D chromatin organizations and found that these changes were strongly associated with perturbed chromatin accessibility and transcriptional dysregulations. Although some discrepancies exist between TNBC cell lines and tissues, we observed that perturbed local 3D architectures found in TNBC cells are partially conserved in TNBC tissues. Furthermore, we discovered distinct tissue-specific chromatin loops by comparing normal and TNBC tissues. Collectively, our findings provide important features of 3D chromatin organization in TNBC. Overall design: For Hi-C experiment (cell lines) : Human mammary epithelial cell (HMEC, as a control) and the cell line of 5 breast cancer subtypes, The cell lines were performed the biological replicates. For Hi-C experiment (Tissues) : Five Contralateral breast normal tissue, three triple negative breast cancer (IDC) tissues. Please note that each processed data was generated from all replicates and is linked to the corresponding rep1 sample records.
SAMPLE_TITLE: Hi-C_TNBC_Tissue2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Triple negative breast cancer tissue, patient2"}, {"TAG": "tissue/cell type", "VALUE": "Triple negative breast cancer tissue, patient2"}, {"TAG": "histological subtype", "VALUE": "Triple negative breast cancer IDC"}]
Pool_Member_@attributes_sample_title: Hi-C_TNBC_Tissue2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_TNBC_Tissue2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_TNBC_Tissue8_1.fq.gz", "size": "24933469889", "date": "2021-02-20 19:23:15", "md5": "434eba37205f03f3a023d300412fcb12", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_TNBC_Tissue8_2.fq.gz", "size": "25284618553", "date": "2021-02-20 19:35:37", "md5": "39a2c5d07670aff67c6264d910406162", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13755479", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13755479/SRR13755479", "size": "31994999728", "date": "2021-02-20 20:10:21", "md5": "925924e8ba7548d0b27f7702fc5065d7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13755479.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR013/13755/SRR13755479/SRR13755479.lite.1", "size": "24229308536", "date": "2022-09-12 12:55:55", "md5": "79de21e20265a02cde62b32619c15c1b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]