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

PRJNA719366: Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

来源: NCBI / GSE171382
提交时间: Apr 02 2021
释放时间: May 29 2021
最后更新时间: May 31 2021

概要: Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection

项目整体设计: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

GEN 数据集:
GEND000462
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生长方案: Cells were maintained in DMEM supplemented with 10%FBS
处理方案: Knockdown was induced by treatment with 1ug/ml Doxycyclin; Cells were seeded into 2.5x10^5/well into 24well plates and infected at MOI=0.1 for 24hpi
提取方案: 24hpi cells were detached and lysed in Trizol LS, total RNA extraction was performed following manufacturers recommendation RNA sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturers guidelines. Briefly, 100ng of total RNA was first depleted of the abundant ribosomal RNA present in the samples by rRNA targeted DNA probe capture followed by enzymatic digestion. Samples were then purified by Beckman Coulter RNAClean XP beads (Cat #A63987). Obtained rRNA-depleted RNA was fragmented, reverse transcribed, converted to dsDNA, end repaired and A-tailed. The A-tailed DNA fragments were ligated to anchors allowing for PCR amplification with Illumina dual indexing primers (Cat#20040553)
建库方案: Libraries were pooled in equimolar concentrations and sequenced on an Illumina NextSeq 500 sequencer using a high-output cartridge (Cat# 20024907), generating single 150bp long reads.
测序信息
分子类型: rRNA- RNA
库的片段类型: SINGLE
库的链类型: Forward
测序平台: ILLUMINA
测序仪型号: Illumina NextSeq 500
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
Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.
Journal of immunology (Baltimore, Md. : 1950) . 2021-05-28 [PMID: 34049971]