1. SciScore for 10.1101/2021.06.07.21258350: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: The collection of bronchial epithelial cells and their study to investigate airway epithelium physiopathology were specifically approved by the Ethics Committee of the Istituto Giannina Gaslini following the guidelines of the Italian Ministry of Health (registration number: ANTECER, 042-09/07/2018).
    IRB: The collection of bronchial epithelial cells and their study to investigate airway epithelium physiopathology were specifically approved by the Ethics Committee of the Istituto Giannina Gaslini following the guidelines of the Italian Ministry of Health (registration number: ANTECER, 042-09/07/2018).
    Consent: Each patient provided informed consent to the study using a form that was also approved by the Ethics Committee.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Rabbit anti-PTX3 antibody was produced in house (Bottazzi et al., 1997), rabbit anti-MBL Ab was purchased from Abcam.
    anti-PTX3
    suggested: None
    Anti-C1q polyclonal antibody was purchased from Dako.
    Anti-C1q
    suggested: (Agilent Cat# F0254, RRID:AB_2335713)
    Anti-CRP and anti-SAP antibodies were from Merck.
    Anti-CRP
    suggested: None
    anti-SAP
    suggested: None
    Bound MBL was detected by incubation with rabbit anti-MBL antibody, followed by HRP-conjugated secondary antibody and TMB development, as described above.
    anti-MBL
    suggested: None
    After washing, C5b-9 deposition was assayed by incubation for 1 h at 37°C with rabbit anti-sC5b-9 antibody (ComplemenTech Inc.,
    anti-sC5b-9
    suggested: None
    Cells were then incubated for 2 h in blocking buffer with the following primary antibodies: mouse anti-cytokeratin 14 (Krt14) (#LL002; 1µg/ml; cat.
    anti-cytokeratin
    suggested: (Leica Biosystems Cat# RTU-LL002, RRID:AB_563793)
    Krt14
    suggested: None
    After washing with PBS and 0.05% Tween, cells were incubated for 1 h with the following species- specific cross-adsorbed secondary antibodies form Invitrogen-ThermoFisher Scientific: donkey anti-rabbit IgG Alexa Fluor® 488 (1µg/ml; cat. N° A-21206); donkey anti-rat IgG Alexa Fluor® 594 (1µg/ml; cat. N° A-21209); donkey anti-mouse IgG Alexa Fluor® 647 (1µg/ml; cat. N° A-31571). 4′,6-diamidino-2-phenylindole (DAPI) (Invitrogen) was used for nucleus staining.
    anti-rabbit IgG
    suggested: (Thermo Fisher Scientific Cat# A-21206, RRID:AB_2535792)
    anti-rat IgG
    suggested: (Thermo Fisher Scientific Cat# A-21209, RRID:AB_2535795)
    anti-mouse IgG
    suggested: (Molecular Probes Cat# A-31571, RRID:AB_162542)
    Experimental Models: Cell Lines
    SentencesResources
    Recombinant human PTX3 and its domains from CHO cells were produced in house, as previously described (Bottazzi et al., 1997).
    CHO
    suggested: None
    Recombinant RBD and trimeric Spike were produced in EXPI293 cells and purified as reported (De Gasparo et al., 2021).
    EXPI293
    suggested: RRID:CVCL_D615)
    Pseudotyped virus production: Human embryonic kidney 293T cells were transfected with a lentiviral vector expressing the Green Fluorescent Protein (GFP) under the control of a human Phosphoglycerate Kinase promoter (PGK) (Cesana et al., 2014) and a pCMV expressing vector containing the SARS-CoV-2 Spike sequence (accession number MN908947) that was codon- optimized for human expression and contained a deletion at the 3’ end aimed at deleting 19 amino acid residues at the C-terminus.
    293T
    suggested: None
    Secondary viral stocks were generated by infection of adherent Vero E6 cells seeded in a 25 cm2 tissue culture flask with 0.5 ml of the primary isolate diluted in 5 ml of complete medium.
    Vero E6
    suggested: None
    After 48 and 72 h post-infection (PI), cell culture supernatants were collected and stored at – 80 °C until determination of the viral titers by a plaque-forming assay in Vero cells.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Briefly, virus incubation with MBL was performed as described above whereas Calu-3 cells were incubated with 10-fold serial dilutions of MBL (from 0.01 to 10 µg/ml – 0.034-34 nM).
    Calu-3
    suggested: None
    Recombinant DNA
    SentencesResources
    Pseudotyped virus production: Human embryonic kidney 293T cells were transfected with a lentiviral vector expressing the Green Fluorescent Protein (GFP) under the control of a human Phosphoglycerate Kinase promoter (PGK) (Cesana et al., 2014) and a pCMV expressing vector containing the SARS-CoV-2 Spike sequence (accession number MN908947) that was codon- optimized for human expression and contained a deletion at the 3’ end aimed at deleting 19 amino acid residues at the C-terminus.
    pCMV
    suggested: RRID:Addgene_20783)
    Software and Algorithms
    SentencesResources
    Reference distances (∼ 40 Å) between mannose molecules were computed in PYMOL.
    PYMOL
    suggested: (PyMOL, RRID:SCR_000305)
    The human lung epithelial Calu-3 cell line was obtained from NovusPharma.
    NovusPharma
    suggested: None
    STED images were de-convolved with Huygens Professional software (Scientific Volume Imaging B. V.; version 19.10) and presented as MIP.
    Huygens Professional
    suggested: None
    Next, we accurately checked cases and controls for solving within-Italian relationships and for testing the possible existence of population stratification within and across batches: to this aim, we performed principal component analysis (PCA), using a LD-pruned subset of SNPs across chromosome 10 and the Plink v.
    Plink
    suggested: (PLINK, RRID:SCR_001757)
    Statistical analysis: Prism GraphPad software v.
    Prism GraphPad
    suggested: None
    1.07 (Purcell et al., 2007); ii) by an unsupervised approach by means of the Beagle software v3.3 (http://faculty.washington.edu/browning/beagle/b3.html), which uses the method described by Browning & Browning (Browning and Browning, 2007) for inferring haplotype phase.
    Beagle
    suggested: (BEAGLE, RRID:SCR_001789)

    Results from OddPub: Thank you for sharing your data.


    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 26. 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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.


    About SciScore

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