EXPERIMENT_TITLE: HiC_Lib_HMS001_JQ1_R1
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To determine human-viral hybrid extrachromosomal DNA (hybrid ecDNA) status, we performed WGS and RNA-seq on 2 HPVOPC cell lines, HMS001 and SCC154, and 2 patient-derived xenograft (PDX) tumors from clinical tumor samples of HPVOPC patients, described here as PDX_A and PDX_C. In addition, long read sequencing for HMS001 and PDX_A that had hybrid ecDNA were also performed.To elucidate chromatin status of hybrid ecDNA, we performed ChIP-seq for H3K27ac (activation mark), H3K4me1 (enhancer mark), and H3K4me3 (promoter mark), and ATAC-seq on HPVOPC cell lines and PDX tumors. To elucidate enhancer and HPV DNA interactions in hybrid ecDNA, HiC-seq was performed using the same cell lines and PDX tumors. Comparison between DMSO and JQ1 treatment of ChIP-seq data or HiC-data are included.
SAMPLE_TITLE: HiC_HMS001_JQ1_R1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "Cell line"}, {"TAG": "age", "VALUE": "NA"}, {"TAG": "biomaterial_provider", "VALUE": "James Rocco"}, {"TAG": "collection_date", "VALUE": "NA"}, {"TAG": "geo_loc_name", "VALUE": "USA: San Diego"}, {"TAG": "sex", "VALUE": "NA"}, {"TAG": "tissue", "VALUE": "pharynx"}, {"TAG": "cell_line", "VALUE": "HMS003"}, {"TAG": "cell_subtype", "VALUE": "hybrid"}, {"TAG": "cell_type", "VALUE": "cancer"}, {"TAG": "culture_collection", "VALUE": "not applicable"}, {"TAG": "dev_stage", "VALUE": "NA_sample_57"}, {"TAG": "disease", "VALUE": "HPVOPC"}, {"TAG": "disease_stage", "VALUE": "NA"}, {"TAG": "ethnicity", "VALUE": "NA"}, {"TAG": "health_state", "VALUE": "NA"}, {"TAG": "karyotype", "VALUE": "NA"}, {"TAG": "phenotype", "VALUE": "NA"}, {"TAG": "population", "VALUE": "NA"}, {"TAG": "race", "VALUE": "NA"}, {"TAG": "sample_type", "VALUE": "cell culture"}, {"TAG": "treatment", "VALUE": "JQ1"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: HiC_HMS001_JQ1_R1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_HMS001_JQ1_R1
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