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Extensive proteomic dataset of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus at Day 4 post-infection

ABSTRACT: Next-generation proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus for defining relevant viral peptides for detection. Cells from Day4 post-infection at 0.01 multiplicity of infection.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Betacoronavirus Sp. (ncbitaxon:1928434) Chlorocebus Aethiops Aethiops (ncbitaxon:101841)

SUBMITTER: Jean Armengaud

PROVIDER: MSV000085509 | MassIVE | Fri May 29 16:10:00 BST 2020

SECONDARY ACCESSION(S): PXD018804

REPOSITORIES: MassIVE

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Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.

Gouveia Duarte D Grenga Lucia L Gaillard Jean-Charles JC Gallais Fabrice F Bellanger Laurent L Pible Olivier O Armengaud Jean J

Proteomics 20200621 14

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyz ...[more]

PMID: 32462744

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Extensive proteomic dataset of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus at Day 4 post-infection

Project description:Next-generation proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus for defining relevant viral peptides for detection. Cells from Day4 post-infection at 0.01 multiplicity of infection.

2020-05-29 | PXD018804 | Pride

PXD018804-1 Extensive proteomic dataset of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus at Day 4 post-infection [Reanalysis: PXD018804]

2023-03-25 | RPXD034693 | JPOST Repository

Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus

Project description:Next-generation proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus for defining the kinetics of whole viral particle antigen production for vaccines. Cells from Day1, Day2, Day3, Day4, Day7 post-infection at two multiplicities of infection.

2020-06-03 | PXD018594 | Pride

Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus

2020-05-29 | MSV000085510 | MassIVE

PXD018594-1 Shotgun proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus [Reanalysis: PXD018594]

2023-03-25 | RPXD034694 | JPOST Repository

RNA-Seq Quantitative Analysis of the regulation of SARS-CoV-2 infection on autophagy and apoptosis related gene transcriptome in infected cells

Project description:In our study, we found that SARS-CoV-2-S pseudovirions infection induced high levels of autophagy and apoptosis in infected cells. To further investigate the underlying regualtion of SARS-CoV-2-S pseudovirions infection in infected cells, ACE2-expressing HEK293T-hACE2 and Vero E6 cells were treated with Mock or SARS-CoV-2-S pseudovirions for RNA-Seq analysis to exame the expression of autophagy- and apoptosis-related genes. Our results indicate that the majority of autophagy- and apoptosis-promoting genes were significantly increased in SARS-CoV-2-S pseudovirions treated HEK293T-hACE2 and Vero E6 cells. In contrast, the subset of autophagy- and apoptosis-suppressing genes was significantly decreased in SARS-CoV-2-S pseudovirions-treated HEK293T-hACE2 and Vero E6 cells than Mock-treated HEK293T-hACE2 and Vero E6 cells. Meanwhile, SARS-CoV-2-S pseudovirions infection enhanced the expression of pro-inflammatory cytokines in infected cells.

2021-03-23 | GSE169370 | GEO

Gene expression of SARS-CoV-2-infected Vero E6 cells

Project description:We conducted a high-throughput drug repositioning screen using the LOPAC®1280 and the ReFRAME drug libraries to identify existing drugs that harbor antiviral activity against SARS-CoV-2, in a Vero E6 cell-based assay. We additionally performed RNA sequencing on control and SARS-CoV-2 infected Vero E6 cells to study the biological changes after SARS-CoV-2 infection and to elucidate the potential mechanisms underlying the positive hits identified from our high-throughput screen. Vero E6 cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI = 0.3) with three replicates. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2020-07-08 | GSE153940 | GEO

Transcriptome analysis to SARS-CoV-2 infection in Vero E6 cells

Project description:RNAseq was used to identify host and viral transcriptome changes in SARS-CoV-2 infection in Vero E6 cells at 8hpi.

2020-11-21 | GSE161881 | GEO

Gene expression of SARS-CoV-2-infected Vero E6 cells with remdesivir treatment

Project description:RNA sequencing was performed on control and SARS-CoV-2 infected Vero E6 cells, with or without remdesivir treatment to study the biological changes after SARS-CoV-2 infection and to evaluate the effectiveness of remdesivir on the gene expression level. 500,000 Vero E6 cells were seeded in 6-well plates. The following day, the cell medium was replaced with fresh medium supplemented with either DMSO or 1 µM remdesivir, and cells were either mock-infected or infected with SARS-CoV-2 USA-WA1/2020 (MOI=0.3), with three replicates per experimental condition. Cells were harvested 24 hours after infection, and total RNA was extracted using the Qiagen® RNeasy® Plus Mini Kit. The quality of the extracted RNA was assessed with the Agilent® 2100 Bioanalyzer. Libraries were prepared from total RNA following ribosome RNA depletion using standard protocol according to Illumina®. Total RNA sequencing was then performed on the Illumina® NextSeq system; 150bp paired-end runs were performed and 100 million raw reads per sample were generated.

2021-02-02 | GSE165955 | GEO

C4PR_LIV: N-terminomic analysis of SARS-CoV-2-infected Vero E6 cells (Unenriched)

Project description:Many events in viral infection are regulated through post-translational modification. In the case of positive-sense RNA viruses such as SARS-CoV-2 which encodes two viral proteases, proteolytic cleavage of both viral and cellular proteins is crucial for productive viral infection. In this work we study proteolysis in the context of SARS-CoV-2 infection of ACE2-A549 and Vero E6 cells, infected at a multiplicity of infection of 1, with samples harvested at 0,6,12 and 24h post-infection. Neo-N-termini and lysine residues were labelled at the protein level with TMTpro reagents prior to tryptic digestion. For unenriched samples, the trypsin-digested material was then fractionated offline, and analysed by LC-MS/MS for the study of total protein abundance over the infection timecourse. For enriched samples, unblocked neo-N-termini generated by tryptic digested were labelled with undecanal and depleted, yielding a sample enriched for blocked neo-N-termini (TMTpro, N-terminal acetylation, and pyroGlu). The enriched samples were similarly fractionated offline and analysed by LC-MS/MS. Please note this is one of several linked datasets. This dataset contains data from Vero E6 cells infected with SARS-CoV-2, prior to enrichment.

2021-07-29 | PXD021154 | Pride

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