EXPERIMENT_TITLE: GSM5241750: Prostate-VCaP-HiC-2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, or according to established protocols (Goloshi. et.al doi: 10.1016/j.ymeth.2018.04.033) Manufacturer's protocol A160141 v01 for library amplification from Arima was used along the NEBNext Ultra II kit (NEB E7645S).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Through a systematic analysis of chromosome conformation capture in a cohort of cells that model cancer progression, San Martin et.al. find that rearrangement of the 3D genome structure in prostate cancer is a potential mechanism for disease exacerbation and that genome-wide compartment identity can classify cancer according to progression Overall design: Analysis of the 3D genomic structure of a cohort of cell lines in the continuum of prostate cancer, from normal to metastatic Pleaes note that each processed data *tar file was generated from all replicates and is linked to the corresponding '*HiC-1' sample records.
SAMPLE_TITLE: Prostate-VCaP-HiC-2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "VCaP cells (ATCC CRL-2876). Vertebral metastastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "ATCC CRL-2876"}, {"TAG": "cell line", "VALUE": "VCaP"}, {"TAG": "source tissue/cell type", "VALUE": "Vertebral metastastatic prostate cancer"}, {"TAG": "condition", "VALUE": "Cells grown under control conditions"}, {"TAG": "media", "VALUE": "DMEM-F12 Ham 1:1, 10%FBS, 100 \uf06dg/ml penicillin-streptomycin."}]
Pool_Member_@attributes_sample_title: Prostate-VCaP-HiC-2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-VCaP-HiC-2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239819.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239819/SRR14239819.lite.1", "size": "2254563781", "date": "2022-07-25 11:54:12", "md5": "1d97ad631b236caababb97d96d6beb3b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239819", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239819/SRR14239819", "size": "2641314465", "date": "2021-04-14 19:34:18", "md5": "d03aac1f7c8da18b1697b10060217177", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Arima2-R1_S10_L001_R2_001.fastq.gz", "size": "2395449371", "date": "2021-04-14 19:33:33", "md5": "b2a706e0e308dda77758c98b68209669", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Arima2-R1_S10_L001_R1_001.fastq.gz", "size": "2346181942", "date": "2021-04-14 19:33:14", "md5": "96e5e95b7a1a3bf9385a0b0acc28ba3a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]