Gene Expression
Nebulas
Gene Expression NebulasSummary: Antiviral therapies targeting the pandemic coronavirus disease 2019 (COVID 19) are urgently required. We studied an already approved botanical drug cepharanthine (CEP) in a cell culture model of GX_P2V, a severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) related virus. RNA sequencing results showed the virus perturbed the expression of multiple cell stress responses such as endoplasmic reticulum (stress and HSF1 mediated heat shock response related genes and signaling pathways, of which heat shock response related genes and pathways were at the core. CEP was potent to reverse most dysregulated genes and pathways in infected cells mainly by interfering with cellular stress responses including ER stress unfolded protein response and HSF 1 mediated heat shock response . Additionally, single cell transcriptomes from COVID 19 patients (GSE150728 and GSE148829) also confirmed that cellular stress responses and stress induced autophagy play an important role in the development of COVID 19. In summary, this study uncovered the potential mechanisms of the anti-viral activities of CEP, providing evidence for CEP as a promising therapeutic option and modulating cellular stress could be a promising therapy for SARS CoV 2 infection
Overall Design: Vero E6 cells (1.5×10e7 cells/flask) were plated in T75 culture flasks for 24h. Cells were treated with GX_P2V, CEP, or CEP and virus, and then cultured for another 72h. Cells were harvested and mRNA was isolated by using TRIzon (Invitrogen). The libraries were constructed by using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) standard protocols. The libraries were sequenced on HiSeq 2500 sequencing system (Illumina)
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| Growth Protocol: | Vero E6 cells (1.5×107 cells/flask) were plated in T75 culture flasks for 24h. |
| Treatment Protocol: | Cells were treated with GX_P2V (2019-nCoVr at MOI = 0.01), CEP (5 uM), or CEP and virus, and then cultured for another 72h. |
| Extract Protocol: | Cells were harvested and mRNA was isolated by using TRIzon (Invitrogen). |
| Library Construction Protocol: | The libraries were constructed by using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) standard protocols. |
| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| 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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