EXPERIMENT_TITLE: GSM5241753: Prostate-MDAPCA2a-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-MDAPCA2a-HiC-2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MDAPCa2a cells (Navone. MD Anderson, Houston TX). Bone metastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "Navone. MD Anderson, Houston TX"}, {"TAG": "cell line", "VALUE": "MDAPCa2a"}, {"TAG": "source tissue/cell type", "VALUE": "Bone metastatic prostate cancer"}, {"TAG": "condition", "VALUE": "Cells grown under control conditions"}, {"TAG": "media", "VALUE": "HPC1 Media, 10%FBS, 100 \uf06dg/ml penicillin-streptomycin."}]
Pool_Member_@attributes_sample_title: Prostate-MDAPCA2a-HiC-2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-MDAPCA2a-HiC-2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-MDA2A-ArimaC-R2_S1_L001_R1_001.fastq.gz", "size": "8828307542", "date": "2021-04-16 02:31:15", "md5": "a3059e87899c8d4b52babce5c3565dff", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-MDA2A-ArimaC-R2_S1_L001_R2_001.fastq.gz", "size": "9395162886", "date": "2021-04-16 02:32:15", "md5": "58360b116ad4f705f3abbd76e9d53253", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239822", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239822/SRR14239822", "size": "13830152736", "date": "2021-04-16 03:16:23", "md5": "4bffa49f18afdfdcf8f0c2859e5b24c8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239822.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239822/SRR14239822.lite.1", "size": "10742086764", "date": "2022-07-25 12:09:09", "md5": "42fcf5fa0275c0bf9380e0fa46a4be0d", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]