EXPERIMENT_TITLE: GSM5241754: Prostate-MDAPCa2B-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-MDAPCa2B-HiC-1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MDAPCa2b cells (Navone. MD Anderson, Houston TX). Bone metastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "Navone. MD Anderson, Houston TX"}, {"TAG": "cell line", "VALUE": "MDAPCa2b"}, {"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-MDAPCa2B-HiC-1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-MDAPCa2B-HiC-1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239823.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239823/SRR14239823.lite.1", "size": "9016981997", "date": "2022-07-27 07:09:55", "md5": "18de1ed926f9dfa4b8e50396448c3657", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239823", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239823/SRR14239823", "size": "11967400489", "date": "2021-04-16 03:20:23", "md5": "79bd3c8abfb7343f9f1c3e4cbfadb8a9", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-MDA2B-ArimaC-R1_S2_L001_R2_001.fastq.gz", "size": "7614243822", "date": "2021-04-16 02:33:47", "md5": "15fab7ec8c8f2504f7439f0f8bcd12f3", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Prostate-MDA2B-ArimaC-R1_S2_L001_R1_001.fastq.gz", "size": "6897665292", "date": "2021-04-16 02:31:20", "md5": "636cddb28f68dd21cc61f46b9d7008c8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]