EXPERIMENT_TITLE: PDX Hi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Two replicated Hi-C datasets of carboplatin-resistant UCD52 cells, generated using Phase Genomics (Seattle, WA) and Arima Genomics (San Diego, CA) library preparation strategies. FASTQ files contain primarily human reads, with some proportion of mouse reads.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "mouse"}, {"TAG": "age", "VALUE": "NA"}, {"TAG": "biomaterial_provider", "VALUE": "Department of Pathology, 1101 E. Marshall Street, Richmond, VA 23298-0662"}, {"TAG": "sex", "VALUE": "not collected"}, {"TAG": "tissue", "VALUE": "solid tissue"}, {"TAG": "Library", "VALUE": "Phase Genomics library preparation"}, {"TAG": "Replicate", "VALUE": "Replicate1"}, {"TAG": "cell_line", "VALUE": "UCD52"}, {"TAG": "cell_subtype", "VALUE": "Carboplatin-resistant"}, {"TAG": "cell_type", "VALUE": "Triple-negative breast cancer"}, {"TAG": "Cultures_collection", "VALUE": "Patient-derived xenograft"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "105244_R1.fastq.gz", "size": "31371028855", "date": "2020-10-20 03:32:17", "md5": "1d617e496bff373fc38fdaae3b53af3b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "105244_R2.fastq.gz", "size": "32253940154", "date": "2020-10-20 03:36:31", "md5": "27da7862fa06280e035b5de6eed32302", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12833499", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12833499/SRR12833499", "size": "45880319283", "date": "2020-10-20 03:47:45", "md5": "9a5362e59c1105cdbe98a80080c449ed", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12833499.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR012/12833/SRR12833499/SRR12833499.lite.1", "size": "34922168727", "date": "2022-07-20 20:45:37", "md5": "42fd0b88db0c9ce786cd4bf024d7791a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]