EXPERIMENT_TITLE: GSM5241746: Prostate-DU145-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-DU145-HiC-2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "DU145 cells (ATCC HTB-81). Brain metastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "ATCC HTB-81"}, {"TAG": "cell line", "VALUE": "DU145"}, {"TAG": "source tissue/cell type", "VALUE": "Brain metastatic prostate cancer"}, {"TAG": "condition", "VALUE": "Cells grown under control conditions"}, {"TAG": "media", "VALUE": "DMEM, 10%FBS, 100 \uf06dg/ml penicillin-streptomycin."}]
Pool_Member_@attributes_sample_title: Prostate-DU145-HiC-2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-DU145-HiC-2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239815.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239815/SRR14239815.lite.1", "size": "19258942784", "date": "2022-07-27 08:14:53", "md5": "745f2c9477931af1f18e9df1536b5dd6", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239815", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239815/SRR14239815", "size": "33086657772", "date": "2021-04-15 03:58:04", "md5": "5166208bc2a74327e73ab1fedb2cd615", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145-61_R2_001.fastq.gz", "size": "23383348971", "date": "2021-04-15 03:18:29", "md5": "105df055846c1bb1a18a26279fe0387d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145-61_R1_001.fastq.gz", "size": "23536397151", "date": "2021-04-15 03:03:48", "md5": "d3dfce90641f11ff5daea0fc9f46c305", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]