EXPERIMENT_TITLE: GSM5241751: Prostate-VCaP-HiC-3; 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-3
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-3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-VCaP-HiC-3
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239820.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239820/SRR14239820.lite.1", "size": "36513435918", "date": "2022-07-25 12:20:51", "md5": "642806e0a77e92b165546d4fbcc20570", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239820", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239820/SRR14239820", "size": "47420020234", "date": "2021-04-15 10:44:19", "md5": "a8be32f5eaab95c44d3324db580149f8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Arima-R1_L001_R2_001.fastq.gz", "size": "37976164860", "date": "2021-04-15 08:35:47", "md5": "41fcabfbc6e68272c3d30d29bc81db1b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-VCaP-Arima-R1_L001_R1_001.fastq.gz", "size": "35988257237", "date": "2021-04-15 05:54:11", "md5": "e5cd1249b75b920415a7bd5c926600a8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]