1. SciScore for 10.1101/2021.11.29.470440: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: All in vivo experiments described were carried out in strict accordance with good animal practice according to NIH recommendations.
    IACUC: All procedures for animal use were approved by the IACUC Committee at Omeros, Inc. (Seattle, WA, USA) and under an approved protocol.
    Sex as a biological variableCD-1 female mice (Charles River Laboratories) 6-8 weeks of age were used for immunological studies performed at the vivarium facilities of Omeros Inc. (Seattle, WA).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Fluorescent-conjugated anti-mouse antibodies used for labeling included CD8β antibody (clone H35-17.2, ThermoFisher), CD4 (clone RM4-5, BD), IFN-γ (clone XMG1.2, BD), TNF-α (clone MP6-XT22, BD) and IL-2 (clone JES6-5H4; BD), and staining was performed in the presence of unlabeled anti-CD16/CD32 antibody (clone 2.4G2; BD).
    anti-mouse
    suggested: None
    CD4
    suggested: (BioLegend Cat# 391503, RRID:AB_2721611)
    IFN-γ
    suggested: None
    TNF-α
    suggested: (Leinco Technologies Cat# T698, RRID:AB_2737572)
    IL-2
    suggested: None
    anti-CD16/CD32
    suggested: None
    The cells (2-4 × 105 cells per well of a 96-well plate) were added to the ELISpot plate containing an immobilized primary antibody to either IFN-γ or IL-4 (BD Cat# 551881 and BD Cat# 551878, respectively), and were exposed to various stimuli (e.g. control peptides SIV and ConA, S-WT and N peptides pools – see catalog numbers above) at a concentration of 1-2 μg/mL peptide pools for 36-40 hours.
    IL-4
    suggested: (BD Biosciences Cat# 551878, RRID:AB_2336921)
    ELISA for detection of antibodies: For IgG antibody detection in inoculated mouse sera and lung homogenates, ELISAs for spike-binding (including S1 Delta) and nucleocapsid-binding antibodies and IgG subclasses (IgG1, IgG2a, IgG2b, and IgG3) were used.
    IgG1, IgG2a
    suggested: None
    IgG3
    suggested: None
    After incubation, the wells were washed with PBST and 100 μL of a 1/5000 dilution of anti-mouse IgG HRP (GE Health Care; Cat # NA9310V), anti-mouse IgG1 HRP (Sigma; Cat # SAB3701171), anti-mouse IgG2a HRP (Sigma; Cat # SAB3701178), anti-mouse IgG2b HRP (Sigma; catalog# SAB3701185), anti-mouse IgG3 HRP conjugated antibody (Sigma; Cat # SAB3701192), or anti-mouse IgA HRP conjugated antibody (Sigma; Cat # A4789) was added to wells.
    anti-mouse IgG
    suggested: None
    anti-mouse IgG1
    suggested: None
    anti-mouse IgG2a
    suggested: None
    anti-mouse IgG2b
    suggested: None
    anti-mouse IgG3
    suggested: None
    anti-mouse IgA HRP
    suggested: None
    Calculation of relative ng amounts of antibodies and the Th1/Th2 IgG subclass bias: A standard curve of IgG for OD vs. ng mouse IgG was generated using purified mouse IgG (Sigma Cat #15381; absorbance values were converted into mass equivalents for both anti-S and anti-N antibodies.
    anti-S
    suggested: None
    anti-N
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Serum-virus mix was then added in duplicate to seeded hACE2 expressing HEK293 cells (BEI Resources) and incubated at 37°C, 5% CO2 for 72 hours.
    HEK293
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Murine immunization and blood/tissue collection: The design of vaccination study performed using CD-1 mice is shown in Figure 2.
    CD-1
    suggested: None
    Software and Algorithms
    SentencesResources
    Fluorescent-conjugated anti-mouse antibodies used for labeling included CD8β antibody (clone H35-17.2, ThermoFisher), CD4 (clone RM4-5, BD), IFN-γ (clone XMG1.2, BD), TNF-α (clone MP6-XT22, BD) and IL-2 (clone JES6-5H4; BD), and staining was performed in the presence of unlabeled anti-CD16/CD32 antibody (clone 2.4G2; BD).
    ThermoFisher
    suggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)
    Flow cytometry was performed using a Beckman-Coulter Cytoflex S flow cytometer and analyzed using Flowjo Software.
    Flowjo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analyses and graph generation: All statistical analyses were performed and graphs generated used in figures were generated using GraphPad Prism software.
    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: 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.
    • No funding statement was detected.
    • 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.

    Read the original source
    Was this evaluation helpful?