EXPERIMENT_TITLE: GSM5241749: Prostate-VCaP-HiC-1; 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-1
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-1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-VCaP-HiC-1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239818.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239818/SRR14239818.lite.1", "size": "2408246168", "date": "2022-07-25 11:54:41", "md5": "360426bc26fac11557bbd2922ab0a96f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239818", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239818/SRR14239818", "size": "2854709592", "date": "2021-04-14 19:55:44", "md5": "cce9941714c65d579a8663a40e189e3e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Control-R1_S8_L001_R2_001.fastq.gz", "size": "2596325862", "date": "2021-04-14 19:47:28", "md5": "675b2bd4752504aca4ec94b34f220554", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Control-R1_S8_L001_R1_001.fastq.gz", "size": "2513501371", "date": "2021-04-14 19:49:11", "md5": "6162c518addd668b6003513bb58eb4de", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]