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  1. SciScore for 10.1101/2022.05.05.490850: (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

    Secondary antibody incubation was performed at room temperature for 2 hours using Goat Anti-Mouse IgG H&L (31430, Thermo) or Goat Anti-Rabbit IgG H&L (31460, Thermo).
    Anti-Mouse IgG
    suggested: (Thermo Fisher Scientific Cat# 31430, RRID:AB_228307)
    Anti-Rabbit IgG
    suggested: (Thermo Fisher Scientific Cat# 31460, RRID:AB_228341)
    Experimental Models: Cell Lines
    ORF6 variant mutants were constructed by subcloning the construct in a TA backbone, followed by substituting the residues as described before (Edelheit et al, 2009) and cloning in the pCAGGS backbone using EcoRI and XhoI. Cell Lines and cell culture: Human embryonic kidney 293T (HEK293T), A549 lung adenocarcinoma, and HeLa cells were purchased from National Centre for Cell Science (NCCS), and HEK-ACE2, Vero cells were procured from the America Type Culture Collection (ATCC, Bethesda, MD).
    suggested: None
    suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
    Viruses and infection: Infection: SARS-CoV2 (Isolate Hong Kong/VM20001061/2020, NR-52282, BEI Resources, NIAID, NIH) was propagated and titered by plaque assay in Vero E6 cells as described before (Case et al, 2020).
    Vero E6
    suggested: None
    Plasmid transfection: HEK-293T cells (0.1 X 106 cells/well) were seeded in a 24 well plate pre-coated with 0.1 mg/mL poly-L-lysine (P9155-5MG, Sigma-Aldrich) and 24 hours later used for transfection.
    suggested: None
    Similarly, Vero cells were seeded on coverslips in 24 well plates (0.1 X 106 cells/well) for overnight incubation.
    suggested: None
    Similarly, HeLa cells were transfected with 250 ng of RIG I Flag or MAVS Flag and 250 ng of ORF6 strep for 24 hours.
    suggested: None
    Recombinant DNA
    For constructing the deletion mutants, the desired sequence was PCR amplified from pLVX-EF1alpha-SARS-CoV-2-ORF6-2xStrep-IRES-Puro plasmid, followed by cloning in the pCAGGS backbone using EcoRI (ER0271, Thermo scientific) and XhoI (ER0691, Thermo scientific) restriction enzyme including the full-length ORF6.
    suggested: RRID:Addgene_141387)
    suggested: RRID:Addgene_127347)
    Luciferase Reporter Assay: For the IFN induction assay, HEK-293T cells were co-transfected, in duplicates, with 50 ng of IFNβ-luc firefly luciferase reporter plasmid, and 20 ng of pRL-TK Renilla luciferase reporter plasmid along with 500 ng of SARS-CoV-2 protein expression plasmid or empty vector.
    pRL-TK Renilla luciferase reporter
    suggested: RRID:Addgene_12179)
    They were then co-transfected with 500 ng of IRF3-GFP and 500 ng of SARS-CoV-2 protein-expressing plasmid using Lipofectamine 2000 reagent (11668019, Invitrogen).
    SARS-CoV-2 protein-expressing
    suggested: None
    Software and Algorithms
    Graphical representations and statistical analysis: All numerical data of luciferase assays and qRt-PCR were analysed and plotted using GraphPad Prism v8.0.2.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The model diagram of ORF6 action (Fig 7) and 3-D structure (Sup Fig 3C) were made by using Biorender
    suggested: (Biorender, RRID:SCR_018361)

    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 did not find any issues relating to the usage of bar graphs.

    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.

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