EXPERIMENT_TITLE: GSM5966530: A549-ACE2 poly-IC rep2 Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Lysates were clarified from sonicated nuclei and biotin-labelled DNA were isolated with C1 beads. DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for Illumina according to manufacturer's instructions.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Many viruses can significantly impact host chromatin, but such roles of SARS-CoV-2 are unknown. Here, we characterized the three-dimensional (3D) genome architecture and epigenome landscapes in human cells after SARS-CoV-2 infection, revealing remarkable restructuring of host chromatin architectures. Overall design: We utlizied Hi-C 3.0, spike-in calibrated ChIP-Seq to map the alterations of 3D genome and epigenome in SARS-CoV-2 infected human cells
SAMPLE_TITLE: A549-ACE2 poly-IC rep2 Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A549-hACE2"}, {"TAG": "cell line", "VALUE": "A549-hACE2"}, {"TAG": "cell type", "VALUE": "epithelial cell"}, {"TAG": "treatment", "VALUE": "poly(I:C) for 6 hours"}]
Pool_Member_@attributes_sample_title: A549-ACE2 poly-IC rep2 Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: A549-ACE2 poly-IC rep2 Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A549-ACE2-NS99-polyIC-HiC-rep2_R1.fastq.gz", "size": "3493295907", "date": "2022-03-23 02:25:50", "md5": "30b5f7a2955f0560b6647b0facbb7c91", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A549-ACE2-NS99-polyIC-HiC-rep2_R2.fastq.gz", "size": "3551556959", "date": "2022-03-22 22:37:26", "md5": "5e2575429f6bfca0c140d020cb9cf88c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18438223", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18438223/SRR18438223", "size": "3593939835", "date": "2022-03-23 04:43:22", "md5": "532ec09cde8185a35f2ff7a14a74a50b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18438223.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR018/18438/SRR18438223/SRR18438223.lite.1", "size": "2269742235", "date": "2022-08-02 00:27:45", "md5": "b5624823dbe520512ed7401347ce6072", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]