EXPERIMENT_TITLE: Hi-C of homo sapiens (human) liver cells (PHH) of patient 345, infected with adenovirus (BC172), day4, replicate 1
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. We used Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected by either hepatitis B virus (HBV) or adenovirus type 5 (Ad5) virus to show that they adopt different strategies in their respective positioning at active chromatin.
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "PHH_345"}, {"TAG": "age", "VALUE": "7 months"}, {"TAG": "biomaterial_provider", "VALUE": "Corning (reference 454541, lot #345)"}, {"TAG": "sex", "VALUE": "female"}, {"TAG": "tissue", "VALUE": "liver"}, {"TAG": "cell_type", "VALUE": "PHH"}, {"TAG": "disease", "VALUE": "Infected with Ad5"}, {"TAG": "disease_stage", "VALUE": "day4"}, {"TAG": "ethnicity", "VALUE": "caucasian"}, {"TAG": "treatment", "VALUE": "Hi-C without Capture"}, {"TAG": "replicate", "VALUE": "biological replicate 1"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7802503.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR007/802/SRR7802503/SRR7802503.sralite.1", "size": "1103794622", "date": "2020-06-21 09:58:34", "md5": "9ace1c3e062ccfd2805b7f7c075d7cdc", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7802503", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7802503/SRR7802503", "size": "1773351234", "date": "2018-09-07 08:39:07", "md5": "4c6bae89a584b73adcffbe9551f59bc8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_PHH_345_adenovirus_BC172_day4_rep1.end2.gz", "size": "1465915816", "date": "2020-02-20 07:49:52", "md5": "c43c31f24fe4499f429e634abca842ae", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_PHH_345_adenovirus_BC172_day4_rep1.end1.gz", "size": "1400654492", "date": "2020-02-20 00:15:32", "md5": "85f8b6ea2fbe03b7f76b0409c161c673", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]