EXPERIMENT_TITLE: GSM5241745: Prostate-DU145-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-DU145-HiC-1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "DU145 cells (ATCC HTB-81). Brain metastatic prostate cancer"}, {"TAG": "biomaterial_provider", "VALUE": "ATCC HTB-81"}, {"TAG": "cell line", "VALUE": "DU145"}, {"TAG": "source tissue/cell type", "VALUE": "Brain metastatic prostate cancer"}, {"TAG": "condition", "VALUE": "Cells grown under control conditions"}, {"TAG": "media", "VALUE": "DMEM, 10%FBS, 100 \uf06dg/ml penicillin-streptomycin."}]
Pool_Member_@attributes_sample_title: Prostate-DU145-HiC-1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Prostate-DU145-HiC-1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14239814.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14239/SRR14239814/SRR14239814.lite.1", "size": "18960296296", "date": "2022-07-27 08:02:21", "md5": "0ce5064d5b32cd79126c60c23ba36f9e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14239814", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14239814/SRR14239814", "size": "33388540972", "date": "2021-04-15 02:45:18", "md5": "a2231d1c96109c2f6617d1f5d448690d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145-60_R2_001.fastq.gz", "size": "23895242311", "date": "2021-04-15 02:35:59", "md5": "07abe6886526a527c876ce60d6e65cff", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DU145-60_R1_001.fastq.gz", "size": "23790930114", "date": "2021-04-15 02:30:03", "md5": "3409079c0fb2ad34aab2569aab6a0289", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]