EXPERIMENT_TITLE: GSM8120375: DU145_Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiment was conducted using Mbo I, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547). After proximity ligation and fragmentation by COVARIS S220, the sequencing library was generated from fragmented DNA using KAPA HyperPrep Kits following the manufacturer's instructions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To elucidate the regulation of NSD2 in metastatic castration-resistant prostate cancer(CRPC), we performed Hi-C against castration-sensitive prostate cancer cell line LNCaP and metastatic castration-resistant prostate cancer cell lines, PC3 respectively. In metastatic CRPC, we found specific regions of activation with epigenetic changes. Overall design: Hi-C seq for prostate cancer cell lines
SAMPLE_TITLE: DU145_Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "DU145"}, {"TAG": "cell line", "VALUE": "DU145"}, {"TAG": "cell type", "VALUE": "prostate cancer"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: DU145_Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: DU145_Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28167105.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR028/28167/SRR28167105/SRR28167105.lite.1", "size": "11794504148", "date": "2024-02-29 14:58:28", "md5": "1e3e6de72d8bfaf7e90dee150f3aec64", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28167105", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28167105/SRR28167105", "size": "17755412892", "date": "2024-02-29 14:20:49", "md5": "785fc2c4580275a6305ebd22cb73cace", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145_R2.fastq.gz", "size": "16193379973", "date": "2024-02-29 14:17:45", "md5": "431d7c2f16520100bf3af5452d432ef1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145_R1.fastq.gz", "size": "15990269364", "date": "2024-02-29 14:18:31", "md5": "e0ee88728ad077f514f02c30a582628a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]