Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

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

Source: NCBI / GSE162316
Submission Date: Nov 30 2020
Release Date:
Update Date: Nov 22 2021

Summary: 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...

Overall Design: 16 samples were analyzed by sRNA-seq, including replicates (sample name contains 'rep').

GEN Datasets:
GEND000357
Strategy:
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Cell Line:
Protocol
Growth Protocol: 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.
Treatment Protocol: 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.
Extract Protocol: 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.
Library Construction Protocol: 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).
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: SINGLE
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NextSeq 500
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
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Analysis:
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
Publications
A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection.
EMBO reports . 2021-12-16 [PMID: 34914162]