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

PRJNA681515: A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection [RNA-seq]

来源: NCBI / GSE162316
提交时间: Nov 30 2020
释放时间: Nov 20 2021
最后更新时间: Nov 22 2021

概要: SARS-CoV-2 infection results in impaired interferon response in severe COVID-19 patients. However, how SARS-CoV-2 interferes with host immune response is incompletely understood. Here, we sequenced small RNAs from SARS-CoV-2-infected human cells and identified a microRNA (miRNA) derived from a recently evolved region of the viral genome. We show that the virus-derived miRNA produces two miRNA isoforms in infected cells by the enzyme Dicer and they are loaded into Argonaute proteins. more...

项目整体设计: 16 samples were analyzed by sRNA-seq, including replicates (sample name contains 'rep').

GEN 数据集:
GEND000357
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方案
生长方案: Human lung A549-ACE2 cells, which have been modified to stably express ACE2 via lentiviral transduction, were generated in the laboratory of Pr. Olivier Schwartz, (Institut Pasteur, Paris, France). A549-ACE2 2 cells were cultured in high-glucose DMEM media (Gibco) supplemented with 10% Fetal Bovine Serum (FBS; Sigma) and 1% penicillin-streptomycin (P/S; Gibco). Cells were maintained at 37°C in a humidified atmosphere with 5% CO2.
处理方案: Mimics RNAs of CoV2-miR-7a.1 and CoV2-miR-7a.2, or control mimic RNA, were synthesized in vitro (Eurofins Genomics). 1 nM of mimic RNAs were transfected in A549-ACE2 or Caco-2 cells using Lipofectamine RNAiMax (Thermo Fischer Scientific). 24 h post-transfection, cells were treated with or without 100U of human Interferon Alpha 2 (PBL Assay Science) for 8, 16 or 24 h.
提取方案: Cells were then lysed using TRIzol LS reagent (Thermo Fischer Scientific) and RNA was extracted following manufacturer’s instructions. DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. DNAse treated RNA with high RIN value was used to deplete ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6350) as per manufacture’s instructions.
建库方案: 100 ng of Ribosomal-depleted RNAs were then used to generate strand-specific RNA libraries using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S). Multiplexed RNA libraries were quantified using Qubit Fluorometer High Sensitivity dsDNA assay kit (ThermoFisher, Q32851) and sequenced on NextSeq-500 Illumina platform using the NextSeq 500/550 High Output v2 kit 75 cycles (FC-404-2005).
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
A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection.
EMBO reports . 2021-12-16 [PMID: 34914162]