EXPERIMENT_TITLE: GSM5241744: Prostate-LNCaP-HiC; 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-LNCaP-HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "LNCaP cells clone FGC (ATCC CRL-1740) lymph node metastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "ATCC CRL-1740"}, {"TAG": "cell line", "VALUE": "LNCaP clone FGC"}, {"TAG": "source tissue/cell type", "VALUE": "lymph node metastatic prostate cancer"}, {"TAG": "condition", "VALUE": "Cells grown under control conditions"}, {"TAG": "media", "VALUE": "ATCC RPMI, 10%FBS, 100 \uf06dg/ml penicillin-streptomycin."}]
Pool_Member_@attributes_sample_title: Prostate-LNCaP-HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-LNCaP-HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239813.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239813/SRR14239813.lite.1", "size": "12094266374", "date": "2022-07-25 12:03:37", "md5": "ee1756d9018090efd425e338909d84aa", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239813", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239813/SRR14239813", "size": "15856382194", "date": "2021-04-16 03:15:49", "md5": "8b76c78cdace558b68e7ca3a8bcd2ddb", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-LNCaP-ArimaC-R1_S3_L001_R2_001.fastq.gz", "size": "11549154163", "date": "2021-04-16 03:04:19", "md5": "7c5fd31042b800f509990a34582541c6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-LNCaP-ArimaC-R1_S3_L001_R1_001.fastq.gz", "size": "10792060319", "date": "2021-04-16 02:59:25", "md5": "3ab8f026c3c2d2801d33ba7bc41545ca", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]