Gene Expression
Nebulas
Gene Expression NebulasSummary: To characterize the early immune responses against coronavirus infection, we infected rhesus macaques and hACE2 transgenic mice with SARS-CoV-2 and analyzed the transcriptome of infected and non-infected animals. We infected WT mice with IAV as a normal respiratory virus group. During analysis, we found that S100A8 was dramatically upregulated by SARS-CoV-2 and a mouse coronavirus (mouse hepatitis virus, MHV), but not by other tested viruses. A group of non-canonical neutrophils were also activated during SARS-CoV-2 infection.
Overall Design: WT Rhesus macaques were infected with SARS-CoV-2 intranasally. Lungs were harvested at 0 dpi, 3 dpi, and 5 dpi. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes; WT C57BL/6J mice and hACE2 transgenic mice were infected with IAV and MHV intranasally. Lungs were harvested at 0 hour, 6 hour, 24 hour, 48 hour, 3 day, 5 day, 7 day post-infection. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes. Differentially expressed genes in Lungs of WT Rhesus macaques infected with SARS-CoV-2 and WT mice infected with IAV.
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| Growth Protocol: | All animals were kept and bred in specific pathogen-free conditions.; All animals were kept and bred in specific pathogen-free conditions |
| Treatment Protocol: | Experiments with live SARS-CoV-2 viruses were carried out in the enhanced biosafety level 3 (P3+) facilities. WT Rhesus macaques were inoculated intranasally with SARS-CoV-2 (10^6 TCID50/ml) after anesthesia and lungs were harvested at 0 dpi, 3 dpi and 5 dpi. WT and hACE2 mice were inoculated intranasally with IAV (10^5 TCID50) and MHV (MHV-a59) after anesthesia and lungs were harvested at 0 hour, 6 hour,24, 48hour, 3day, 5day, 7 day post-infection. |
| Extract Protocol: | Lungs were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (Qiagen NO. 74104).The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer's recommendations |
| Library Construction Protocol: | RNA libraries were prepared for sequencing using standard Illumina protocols |
| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | -; Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| Strand-Specific: | Unspecific; 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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