Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA673899: Analysis on Replication and Transcription of SARS-CoV-2 and inhition effect of Remdesivir

来源: NCBI / GSE160668
提交时间: Nov 02 2020
释放时间: Jun 27 2021
最后更新时间: Jul 29 2021

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.

GEN 数据集:
GEND000447
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方案
生长方案: 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.
处理方案: 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.
提取方案: 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)
建库方案: -
测序信息
分子类型: polyA(+) RNA; rRNA- RNA
库的片段类型: PAIRED
库的链类型: Forward; Reverse
测序平台: ILLUMINA
测序仪型号: Illumina NovaSeq 6000
链特异性: Specific
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数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度
文章
The strand-biased transcription of SARS-CoV-2 and unbalanced inhibition by remdesivir.
iScience . 2021-07-14 [PMID: 34278249]