SARS-CoV-2 triggers DNA damage response in Vero E6 cells

  1. Joshua Victor
  2. Jamie Deutsch
  3. Annalis Whitaker
  4. Erica N. Lamkin
  5. Anthony March
  6. Pei Zhou
  7. Jason W. Botten
  8. Nimrat Chatterjee

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Abstract

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  1. Version published to 10.1016/j.bbrc.2021.09.024
  2. ScreenIT

    SciScore for 10.1101/2021.09.08.459535: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Primers: Immunoblotting and Antibodies: Protein lysates from SARS-CoV-2 infected Vero E6 cells were harvested in 2x Laemmli sample buffer (Bio-Rad) containing 2-Mercaptoethanol (Fisher Scientific).
    Antibodies
    suggested: None
    Membranes were blotted with the following antibodies: Actin (Invitrogen, MA1744
    Actin
    suggested: (Thermo Fisher Scientific Cat# MA1-744, RRID:AB_2223496)
    Membranes were washed three times for five minutes each with PBS (Cytia) with 0.1% Tween-20, before and after incubating with secondary antibody for one hour, with donkey anti-mouse (IRDye 680RD, Li-COR BioSciences) or goat anti-rabbit (IRDye 800CW, Li-COR Biosciences), at 1:20,000 with 0.01% SDS and 0.1% Tween-20.
    anti-mouse
    suggested: None
    anti-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Vero E6 cells were infected with SARS-CoV-2 WA1 at an MOI of 0.01 and incubated for 48 hours before collecting the cells for further downstream processing.
    Vero E6
    suggested: None
    Software and Algorithms
    SentencesResources
    RT-qPCR and Telomere Length Assay: Isolated RNA was quantified using the Nanodrop-2000 (ThermoFisher), and then diluted using RNase/DNase free water (VWR Life Sciences) until all the concentration of RNA in each sample was 10ng/µL.
    ThermoFisher
    suggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)
    The StepOnePlus software was used to analyze that data and GraphPad Prism 9.0.1 was used for statistical analysis and to the plot the results.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Membranes were imaged with the Li-COR Odyssey CLx, and images were analyzed with Image Studio software.
    Image Studio
    suggested: (Image Studio Lite, RRID:SCR_013715)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.09.08.459535v1 on bioRxiv