1. SciScore for 10.1101/2021.06.07.447437: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The protocols for human specimen collection were approved by the institutional review board of City of Hope.
    Euthanasia Agents: Mice were euthanized using ketamine (100 mg/kg)/xylazine (10 mg/kg) when body weights dropped below 20% of their original body weights.
    IACUC: Experiments and handling of mice were conducted under federal, state, and local guidelines and with approvals from the Northern Arizona University (20-005) and City of Hope Animal Care and Use Committees.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationContamination: All cell lines were routinely tested to confirm absence of mycoplasma using the MycoAlert Plus Mycoplasma Detection Kit from Lonza (Walkersville, MD).

    Table 2: Resources

    Antibodies
    SentencesResources
    SARS-CoV-2 viral nucleocapsid protein (NP) was detected using the anti-NP protein antibody (PA5-81794, Thermo Fisher) diluted 1:10000 in 0.1% tween-20/1%BSA/PBS solution as a primary antibody, followed by detecting with an anti-rabbit secondary antibody (ab6721, Abcam) at a 1:20,000 dilution.
    SARS-CoV-2 viral nucleocapsid protein ( NP )
    suggested: None
    SARS-CoV-2 viral nucleocapsid protein ( NP
    suggested: None
    PA5-81794
    suggested: (Thermo Fisher Scientific Cat# PA5-81794, RRID:AB_2788968)
    anti-rabbit
    suggested: (Abcam Cat# ab6721, RRID:AB_955447)
    FXa-HRP conjugated anti-human Fc antibody (05-4220, Invitrogen) was used as a detecting antibody.
    anti-human Fc
    suggested: (Thermo Fisher Scientific Cat# 05-4220, RRID:AB_2532922)
    The cells were then washed and incubated with an anti-S protein antibody for 20 minutes at room temperature, followed by staining with a FITC-labeled secondary antibody (111-605-045, Jackson ImmunoResearch).
    anti-S protein
    suggested: None
    An HRP-conjugated anti-His tag antibody (ab1187, Abcam) was used as a detecting antibody.
    An HRP-conjugated anti-His tag antibody
    suggested: None
    anti-His tag
    suggested: None
    IHC staining with an anti-FXa protein antibody (PIPA529118, Invitrogen), an anti-furin antibody (ab183495, Abcam), an anti-trypsin antibody (ab200997, Abcam), or an anti-plasmin antibody (LS-C150813-1, LSBio) as a primary antibody was performed by the Pathology Shared Resource Core at City of Hope Beckman Research Institute.
    anti-FXa protein
    suggested: None
    anti-furin
    suggested: (Abcam Cat# ab183495, RRID:AB_2801581)
    anti-trypsin
    suggested: None
    anti-plasmin
    suggested: None
    H&E staining and IHC with anti-NP protein antibody (NB100-56576, Novus) as the primary antibody were performed by the Pathology Shared Resource Core at City of Hope Beckman Research Institute.
    anti-NP protein antibody
    suggested: (Creative Diagnostics Cat# DPAB-DC4728, RRID:AB_2501850)
    anti-NP protein
    suggested: (Creative Diagnostics Cat# DPAB-DC4728, RRID:AB_2501850)
    NB100-56576
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Monkey kidney epithelium-derived Vero cells, Vero E6 cells, human embryonic kidney-derived HEK293T cells, and Chinese hamster ovary (CHO) cells were cultured in DMEM with 10% FBS, penicillin (100 U/ml), and streptomycin (100 μg/ml).
    Chinese hamster ovary (CHO)
    suggested: None
    To determine viral production, Vero cells were pre-seeded for 24 hours and infected with the supernatants collected from MA104 cells infected by VSV-SARS-CoV at 24 or 48 hpi.
    Vero
    suggested: None
    Generation and purification of FXa: CHO cells were transduced with a pCDH lentiviral vector expressing FXa to produce the FXa-Fc fusion protein for functionality assays.
    CHO
    suggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)
    Virus isolates were passaged in Vero E6 cells (ATCC CRL-1586) as previously described3.
    Vero E6
    suggested: None
    Assessment of binding between S protein and FXa using flow cytometry: HEK293T cells were transduced with lentiviral vector expressing FXa for 48 hours.
    HEK293T
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    In vivo infection model: 6-8-week-old K18-hACE2 mice were anesthetized with ketamine (80 mg/kg)/xylazine (8 mg/kg) and intranasally infected with 5×103 PFU wild type SARS-CoV-2 or B.1.1.7 variant in 25 μl DMEM, followed by intranasal treatment with PBS, FXa-Fc (200 μg), or Fc (200 μg) in 25 μl DMEM.
    K18-hACE2
    suggested: RRID:IMSR_GPT:T037657)
    Recombinant DNA
    SentencesResources
    Pull-down assay: HEK293T cells were transduced with a pCDH lentiviral vector expressing the full-length spike (S) protein for 48 hours.
    pCDH
    suggested: RRID:Addgene_102325)
    Software and Algorithms
    SentencesResources
    Prism software v.8 (
    Prism
    suggested: (PRISM, RRID:SCR_005375)

    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.

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