EXPERIMENT_TITLE: HCC1187
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We developed a new computational framework, HiDENSEC (Hi-C based Direct Estimation of Copy Number and Structural rEarrangements in Cancer cells), to estimate the fraction of cancer cells in mixed samples, infer absolute copy number over the genome, detect and ascribe copy number to large-scale structural variants (LSSVs) using proximity ligation sequencing data from formalin-fixed tumor samples (Fix-C).
SAMPLE_TITLE: HCC1187
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "100% HCC1187"}, {"TAG": "age", "VALUE": "not applicable"}, {"TAG": "biomaterial_provider", "VALUE": "Dirk Hockemeyer"}, {"TAG": "sex", "VALUE": "not applicable"}, {"TAG": "tissue", "VALUE": "not applicable"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: HCC1187
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HCC1187
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR19696029.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR019/19696/SRR19696029/SRR19696029.lite.1", "size": "55367274939", "date": "2022-08-05 16:58:44", "md5": "9348d140d318cedd15888c4e90a8eab9", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR19696029", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR19696029/SRR19696029", "size": "91238463219", "date": "2022-06-18 04:18:05", "md5": "13ffbba7d68e5212a588aa3cc4573440", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HCC1187-HiC1_R2.fastq.gz", "size": "67344848615", "date": "2022-06-18 04:02:43", "md5": "34fdf6bd477438f6249260e0839722cd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HCC1187-HiC1_R1.fastq.gz", "size": "65840045829", "date": "2022-06-18 03:59:15", "md5": "528ef96a67cc22729c3b47fe19f0a4ea", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]