EXPERIMENT_TITLE: GSM5966525: A549-ACE2 HCoV-OC43 rep1 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 HCoV-OC43 rep1 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": "common cold coronavirus HCoV-OC43"}]
Pool_Member_@attributes_sample_title: A549-ACE2 HCoV-OC43 rep1 Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: A549-ACE2 HCoV-OC43 rep1 Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A549-ACE2-NS97-OC43-HiC-rep1_R1.fastq.gz", "size": "4305782545", "date": "2022-03-22 22:18:41", "md5": "ae89d0901cacef4dd1ae399ef25913c2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A549-ACE2-NS97-OC43-HiC-rep1_R2.fastq.gz", "size": "4298970739", "date": "2022-03-22 22:15:53", "md5": "3cd1dd8b00bc6294d5e78e0f3ffd477c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18438218", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18438218/SRR18438218", "size": "4360125351", "date": "2022-03-22 22:32:07", "md5": "0dea9872b8d0a09df602e53ac64f9d9f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18438218.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR018/18438/SRR18438218/SRR18438218.lite.1", "size": "2789191991", "date": "2022-08-08 23:03:27", "md5": "28d92d7eb6480a63e2c7ab70daaacd41", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]