EXPERIMENT_TITLE: GSM7918227: PC3_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: PC3_Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "PC3"}, {"TAG": "cell line", "VALUE": "PC3"}, {"TAG": "cell type", "VALUE": "prostate cancer"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: PC3_Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: PC3_Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PC3_R1_fastq", "size": "212820954294", "date": "2023-11-26 19:19:09", "md5": "4dce1d43f5292c85ff6289d8102766c0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PC3_R2_fastq.gz", "size": "46076811191", "date": "2023-11-26 19:24:12", "md5": "966d65843e90f9fd5938b4ff4b538ee5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR26949824", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26949824/SRR26949824", "size": "58281648737", "date": "2023-11-26 19:36:12", "md5": "597091623696df35e1b96e208dbd45c8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR26949824.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR026/26949/SRR26949824/SRR26949824.lite.1", "size": "45417247733", "date": "2023-11-26 21:31:54", "md5": "d832dc0caeff30ecc9ba176080635e71", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]