EXPERIMENT_TITLE: GSM5013423: Mock infected pCHi-C replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Crosslinking was performed with 2% formaldehyde followed by cell membrane lysis. Lysates were snap frozen and stored at -80C. PCHi-C (Schoenfelder et al., 2015) was combined with Hi-C library generation as described previously (Nagano et al., 2017), with some modifications. Cell lysates were digested with DpnII (NEB) overnight at 37C rotating (950rpm). Restriction overhangs were filled-in with Klenow (NEB) using biotin-14-dATP (Jena Bioscience), and ligation was performed in ligation buffer for 4 hours at 16C (T4 DNA ligase; Life Technologies). After overnight decrosslinking at 65C, the ligated DNA was tagmented to produce fragments of 300-700 bp range. Ligation products were isolated using MyOne C1 streptavidin beads (Life Technologies), followed by washing with Wash&Binding buffer and nuclease-free water. Isolated Hi-C ligation products on the beads were then used directly for PCR amplification, and the final Hi-C library was purified with AMPure XP beads (Beckman Coulter). Promoter Capture Hi-C was performed using a custom-design Agilent SureSelect system following the manufacturer's protocol.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Here, A549 cells expressing the ACE2 receptor were infected with SARS-CoV2, and pCHi-C was performed at 0 (mock), 8 and 24 hours post-infection. This repository provides the raw pCHi-C sequence reads and downstream processed CHiCAGO data (Rds files). Overall design: A549 cells were crosslinked for promoter capture Hi-C (pCHi-C) experiments at zero (mock), eight and twenty-four hours post-infection with the SARS-Cov2 virus. pCHi-C libraries were generated and sequenced using paired-end NGS. This data accompanies the publication "Topoisomerase 1 inhibition therapy protects against SARS-CoV-2- induced inflammation and death in animal models".
SAMPLE_TITLE: Mock infected pCHi-C replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human alveolar basal epithelial carcinoma cell line expressing the human SARS-CoV-2 entry receptor Ace2"}, {"TAG": "cell line", "VALUE": "A549-ACE2"}, {"TAG": "treatment", "VALUE": "None"}, {"TAG": "time point", "VALUE": "0 hours"}]
Pool_Member_@attributes_sample_title: Mock infected pCHi-C replicate 2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Mock infected pCHi-C replicate 2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR13398930.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR013/13398/SRR13398930/SRR13398930.lite.1", "size": "14269208772", "date": "2022-08-10 01:33:56", "md5": "3211a9c6d3a9f175c64b74d7e8090071", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR13398930", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13398930/SRR13398930", "size": "18137493272", "date": "2021-01-11 00:10:29", "md5": "4df888d367d080a0f85b3cc368a9afbd", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "mock_pCHiC_rep2_R2.fastq.gz", "size": "13499970437", "date": "2021-01-10 23:56:21", "md5": "c904896e48ca3f9b0918c6a62a530b91", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "mock_pCHiC_rep2_R1.fastq.gz", "size": "14737169034", "date": "2021-01-11 00:01:50", "md5": "435e5e9012582fde8e28d283689f8f84", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]