PRJNA673899: Analysis on Replication and Transcription of SARS-CoV-2 and inhition effect of Remdesivir
概要: SARS-CoV-2, a betacoronavirus with a positive-sense, single-stranded RNA genome, caused the COVID-19 pandemic with unprecedent health and socio-economic crisis. Although its general sense mRNA architecture was reported, that of its negative strand was unexplored. We combined poly(A)-mRNA and ribosomal RNA-depleted sequencing to delineate several fine features of both RNA strands. Together with the transcriptome data under the perturbation of anti-viral drug Remdesivir, this project opens new sights into SARS-CoV-2 replication mechanism and may facilitate the anti-viral drug design.
项目整体设计: Overall 10 samples are analyzed, six of which are Poly(A) RNA-seq and four are Ribozero RNA-seq samples. Poly(A) RNA-seq samples contain two treatment conditions with triplicates. Ribozero RNA-seq samples contain two treatment conditions with duplicates.
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Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37 °C in a humidified atmosphere of 5% CO2. |
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For virus infection, Vero E6 cells, with 90% confluency in 12-well plates, were inoculated with the SARS-CoV-2 virus at a MOI of 0.05. One hour after incubation at 37 °C, cells were washed three times with phosphate buffered saline (PBS) followed by 24-hours.Remdesivir (Cat. No. HY-104077) was purchased from MedChemExpress (Monmouth Junction, NJ). The SARS-CoV-2 strains used in this research were isolated from COVID-19 patients in Guangzhou (Accession numbers: MT123290 ), and passaged on Vero E6. incubation in the fresh normal culture medium with or without Remdesivir at 10 uM of final concentration. |
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Cultured cells were washed once with PBS before adding TRIzol (Vazyme, Cat no. R401-01). Total RNA extracted according to the manufacturer’s instructions. RNA was eluted in 20 μl RNase-free water.
Purified total RNAs from non-infected and SARS-CoV-2-infected Vero cells were reverse transcribed using the RT SuperMix Reagent Kit with gDNA Eraser (Vazyme, Cat no. R223-01). Briefly, 1 μg total RNA was firstly digested with gDNA eraser to remove contaminated DNA and then the first-strand cDNA was synthesized in 20 μl reaction with Oligo (dT) or forward and reverse PCR primer for negative-strand and positive-strand specific reverse transcription, respectively. Finally, 2 μl ten times diluted cDNA was used as template for quantitative PCR. RT-qPCR was performed on CFX96 Real-time PCR system (Bio-Rad) with the SYBR Green Master Mix (Yeasen, Cat no. 11201ES03) |
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polyA(+) RNA; rRNA- RNA |
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PAIRED |
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Forward; Reverse |
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ILLUMINA |
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Illumina NovaSeq 6000 |
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Specific |
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The strand-biased transcription of SARS-CoV-2 and unbalanced inhibition by remdesivir.
iScience . 2021-07-14 [PMID:
34278249]