1. SciScore for 10.1101/2020.12.23.424169: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was approved by the joint University College London/University College London Hospitals NHS Trust Human Research Ethics Committee and written informed consent was obtained from all participants.
    Consent: The study was approved by the joint University College London/University College London Hospitals NHS Trust Human Research Ethics Committee and written informed consent was obtained from all participants.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cells were then incubated with 1μg/ml CR3009 SARS-CoV-2 cross-reactive antibody (a kind gift from Dr. Laura McCoy,) in permeabilisation buffer for 30 min at room temperature, washed once and incubated with secondary Alexa Fluor 488-Donkey-anti-Human IgG (Jackson Labs).
    488-Donkey-anti-Human IgG
    suggested: None
    A blocking step was carried out for 1h at room temperature with 10% goat serum/1%BSA in PBS. Nucleocapsid (N) proten detection was performed by primary incubation with human anti-N antibody (Cr3009, 1ug/ml) for 18h, and washed thoroughly in PBS.
    anti-N
    suggested: None
    Cr3009
    suggested: None
    Primary antibodies were detected by labelling with with secondary anti-human AlexaFluor488 and anti-rabbit AlexaFluor546 conjugates (Jackson Immuno Research) for 1h.
    anti-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Vero.E6 were provided by NIBSC, Beas2B (ATCC CRL-9609) and Hulec5a (ATCC CRL-3244) were obtained from ATCC, and Detroit 562 (ATCC CCL-138) were a kind gift from Dr Caroline Weight (UCL).
    Hulec5a
    suggested: ATCC Cat# CRL-3244, RRID:CVCL_0A11)
    THP-1 cells were cultured in RPMI (Gibco) supplemented with 10 heat-inactivated FBS (Labtech)
    THP-1
    suggested: None
    Caco-2 and Calu-3 cells were stimulated for 24 h with media containing TLR4 agonist Lipopolysaccharide (LPS) (Peprotech), the TLR3 agonist poly I:C (Peprotech) or the TLR7 agonist R837 (Invivogen), using the concentration stated on each figure.
    Calu-3
    suggested: None
    Virus culture and infection: SARS-CoV-2 strain BetaCoV/Australia/VIC01/2020 (NIBSC) was propagated by infecting Caco-2 cells at MOI 0.01 TCID50/cell, in DMEM supplemented with 2% FBS at 37°C.
    Caco-2
    suggested: None
    Virus titres were determined by 50% tissue culture infectious dose (TCID50) on Vero.E6 cells.
    Vero.E6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Software and Algorithms
    SentencesResources
    All samples were acquired on a BD Fortessa X20 or LSR II using BD FACSDiva software.
    BD FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    Data was analysed using FlowJo v10 (Tree Star).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Image analysis: NF-κB, IRF3, IL6 and GAPDH raw image channels were pre-processed using a batch rolling ball background correction in FIJI imagej software package (Schindelin et al., 2012) prior to quantification.
    imagej
    suggested: (ImageJ, RRID:SCR_003070)
    Statistical analysis: Statistical analysis was performed using GraphPad Prism.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 29. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


    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.

    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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