1. SciScore for 10.1101/2021.08.09.455472: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Isolation of neutrophils from peripheral blood: Neutrophils were isolated from fresh human peripheral blood with patient consent and approval of the Institutional Review Board (IRB) of the University of Southern California (USC), protocol #HS-20-00546.
    IRB: Isolation of neutrophils from peripheral blood: Neutrophils were isolated from fresh human peripheral blood with patient consent and approval of the Institutional Review Board (IRB) of the University of Southern California (USC), protocol #HS-20-00546.
    Sex as a biological variablenot detected.
    RandomizationFor this study, HBEC donors were randomly paired with blood neutrophil donors.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 virus (BEI resources, Manassas, VA) was cultured and passaged 4 times in VeroE6-hACE2 cells and harvested every 48 hours post-inoculation.
    VeroE6-hACE2
    suggested: None
    Serial dilutions of SARS-CoV-2 virus were performed from a stock concentration of 1×105 PFU/ml and inactivated with 1% Triton-X at room temperature for 1 hour and used to infect Vero E6 cells for a total of 4 days.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Calibration curves for RNAseP primers/probe was performed with 10-fold dilutions of RNA from uninfected Calu3 cells (ATCC, Manassas, VA) from 100 ng to 0.01 ng per reaction.
    Calu3
    suggested: None
    Software and Algorithms
    SentencesResources
    Cells were analyzed on the Sorp FACS Symphony cell sorter (BD Biosciences) in the Flow Cytometry Core facility at USC using FACS Diva software and all analyses was carried out in Flow Jo V10.8.0 (BD Biosciences)
    Flow Jo
    suggested: (FlowJo, RRID:SCR_008520)
    Single Cell RNA sequencing and Bioinformatic Analysis:
    Bioinformatic
    suggested: (QFAB Bioinformatics, RRID:SCR_012513)
    We then visualized the range of cluster resolutions using the R package clustree (version 0.4.3) (3).
    clustree
    suggested: (clustree, RRID:SCR_016293)
    Cluster specific cell types were annotated manually by examining the expression of canonical marker genes within a given cluster and clusters with shared marker gene expression patterns were collapsed.
    Cluster
    suggested: (Cluster, RRID:SCR_013505)
    Images were analyzed with ImageJ software 1.52n (National Institute of Health, Bethesda, MA).
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    Data was presented and analyzed using Graph Pad prism v8.4.3 (GraphPad, San Diego, CA).
    GraphPad
    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: We detected the following sentences addressing limitations in the study:
    Using primary human cells in a co-culture of epithelial and inflammatory cells overcomes some of the limitations of more widely used model systems to study SARS-CoV-2 infection. Although considered the gold standard providing the opportunity to study infection in vivo, the relevance of animal models in mimicking human lung pathophysiology is unclear, particularly with respect to SARS-COV-2. To date, although infection can be detected, no animal model had closely reflected COVID-19 pathogenesis that leads to severe symptoms and fatal lung disease (Kumar et al., 2020; Munoz-Fontela et al., 2020). Furthermore, studying neutrophilia in animal models is challenging, several depleted or knockout models exist (Stackowicz et al., 2019), however evaluation of elevated lung neutrophilia typically requires pro-inflammatory stimulation with lipopolysaccharide (LPS) (Corteling et al., 2002), this could complicate interpretation of findings in relation to viral infection. Many studies investigating the cellular and molecular mechanisms of SARS-CoV-2 infection have used studied in cell lines, such as HELA, or HEK cells, which themselves lack expression of ACE2. This limitation is overcome by overexpressing human ACE2, or by using airway epithelial cell lines, such as A549 or CALU3 cells, which are derived from lung cancers and, while epithelial in origin, are limited in their capacity to represent the biology and physiology of a normal differentiated human airway epithelium. In our study, u...

    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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