Summary: SARS-CoV-2 infection results in impaired interferon response in severe COVID-19 patients. However, how SARS-CoV-2 interferes with host immune response is incompletely understood. Here, we sequenced small RNAs from SARS-CoV-2-infected human cells and identified a microRNA (miRNA) derived from a recently evolved region of the viral genome. We show that the virus-derived miRNA produces two miRNA isoforms in infected cells by the enzyme Dicer and they are loaded into Argonaute proteins. more...
Overall Design: 16 samples were analyzed by sRNA-seq, including replicates (sample name contains 'rep').
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Growth Protocol: | Human lung A549-ACE2 cells, which have been modified to stably express ACE2 via lentiviral transduction, were generated in the laboratory of Pr. Olivier Schwartz, (Institut Pasteur, Paris, France). A549-ACE2 2 cells were cultured in high-glucose DMEM media (Gibco) supplemented with 10% Fetal Bovine Serum (FBS; Sigma) and 1% penicillin-streptomycin (P/S; Gibco). Cells were maintained at 37°C in a humidified atmosphere with 5% CO2. |
Treatment Protocol: | Mimics RNAs of CoV2-miR-7a.1 and CoV2-miR-7a.2, or control mimic RNA, were synthesized in vitro (Eurofins Genomics). 1 nM of mimic RNAs were transfected in A549-ACE2 or Caco-2 cells using Lipofectamine RNAiMax (Thermo Fischer Scientific). 24 h post-transfection, cells were treated with or without 100U of human Interferon Alpha 2 (PBL Assay Science) for 8, 16 or 24 h. |
Extract Protocol: | Cells were then lysed using TRIzol LS reagent (Thermo Fischer Scientific) and RNA was extracted following manufacturer’s instructions. DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. DNAse treated RNA with high RIN value was used to deplete ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6350) as per manufacture’s instructions. |
Library Construction Protocol: | 100 ng of Ribosomal-depleted RNAs were then used to generate strand-specific RNA libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S). Multiplexed RNA libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005). |
Molecule Type: | rRNA- RNA |
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Library Layout: | SINGLE |
Library Strand: | Forward |
Platform: | ILLUMINA |
Instrument Model: | Illumina NextSeq 500 |
Strand-Specific: | Specific |
Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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