1. SciScore for 10.1101/2020.08.31.276725: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    ) IgG monoclonal, primary antibodies and AlexaFluor® goat anti-mouse IgG polyclonal antibodies (Dianova; # 115-545-146).
    anti-mouse IgG
    suggested: (Jackson ImmunoResearch Labs Cat# 115-545-146, RRID:AB_2307324)
    Rabbit anti-E-cadherin IgG monoclonal (CellSignaling; 3195S) or rabbit anti-VE-cadherin polyclonal, primary antibodies (CellSignaling; 2158S) and Cy5 goat anti-mouse IgG polyclonal antibodies (Dianova; #111-175-144) were used to detect cell borders of Calu-3 or HUVEC cells on the membrane of the alveolus-on-a-chip model, respectively.
    anti-E-cadherin IgG
    suggested: None
    anti-VE-cadherin
    suggested: (Cell Signaling Technology Cat# 2158, RRID:AB_2077970)
    For the detection of SARS-CoV-2 spike protein a rabbit polyclonal anti-SARS-CoV-2 spike S2 antibody (Sino Biological #40590-T62) was used.
    anti-SARS-CoV-2 spike S2
    suggested: (Thermo Fisher Scientific Cat# PA5-112048, RRID:AB_2866784)
    Experimental Models: Cell Lines
    SentencesResources
    For the cultivation of the human alveolus-on-a-chip model we used Calu-3 cells and macrophages at the epithelial side, and HUVECs at the endothelial side.
    HUVECs
    suggested: None
    For infection of Vero-76 or Calu-3 cells, cells were washed with PBS and either left uninfected (mock) or infected with SARS-CoV-2 with a multiplicity of infection (MOI) of 1 for 120 min in medium (EMEM with HEPES modification and 5 mM L-Glutamine for Vero-76 cells and RPMI 1640 for Calu-3 cells) supplemented with 10 % FCS.
    Vero-76
    suggested: None
    Calu-3
    suggested: None
    Rabbit anti-E-cadherin IgG monoclonal (CellSignaling; 3195S) or rabbit anti-VE-cadherin polyclonal, primary antibodies (CellSignaling; 2158S) and Cy5 goat anti-mouse IgG polyclonal antibodies (Dianova; #111-175-144) were used to detect cell borders of Calu-3 or HUVEC cells on the membrane of the alveolus-on-a-chip model, respectively.
    HUVEC
    suggested: KCB Cat# KCB 200648YJ, RRID:CVCL_2959)
    Software and Algorithms
    SentencesResources
    The cDNA preparation was performed using the SuperScript IV (Thermofisher), followed by a multiplex PCR to generate overlapping 400 nt amplicons using version 3 of the primer set (https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3).
    Thermofisher
    suggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)
    Infection by SARS-CoV-2 was visualized using mouse anti-SARS-CoV-2 spike (GeneTex; #GTX632604
    GeneTex
    suggested: (GeneTex, RRID:SCR_000069)
    Images were acquired using an Axio Observer.Z1 microscope (Zeiss) with Plan Apochromat 20x/0.8 objective (Zeiss), ApoTome.2 (Zeiss) and Axiocam 503 mono (Zeiss) and the software Zen 2.6 (blue edition; Zeiss).
    Zen
    suggested: None
    Fiji V 1.52b (ImageJ) was used for further image processing, including Z-stack merging with maximum intensity projection and gamma correction.
    Fiji
    suggested: (Fiji, RRID:SCR_002285)
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    Statistical analysis: Statistical analyses were performed using Prism 8 (GraphPad Software).
    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: 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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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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