Dissecting the common and compartment-specific features of COVID-19 severity in the lung and periphery with single-cell resolution

  1. Kalon J. Overholt
  2. Jonathan R. Krog
  3. Ivan Zanoni
  4. Bryan D. Bryson

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Abstract

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  1. Version published to 10.1016/j.isci.2021.102738
  2. Version published to 10.1101/2020.06.15.147470v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.15.147470: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Gene set enrichment analysis (GSEA) [67] was performed using the “fgsea” package (v. 1.12.0) [68] in R.
    Gene set enrichment analysis
    suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
    GSEA results were interpreted according to normalized enrichment score (NES) and an adjusted p-value, with a p<0.05 significance threshold.
    GSEA
    suggested: (SeqGSEA, RRID:SCR_005724)
    Transcription factor (TF) analysis was similarly conducted on the DEG list to query the regulation of TFs identified by the ENCODE and ChEA ChIP-X databases [71, 72].
    ENCODE
    suggested: (Encode, RRID:SCR_015482)
    ChEA
    suggested: (ChEA, RRID:SCR_005403)
    To specifically analyze signaling from mononuclear phagocytes and neutrophils, differentially expressed target genes ranking among the 250 most strongly predicted targets of the top 20 ligands were used, with the upper 25% of these targets according to regulatory potential visualized in circos plots.
    circos
    suggested: (Circos, RRID:SCR_011798)
    For each receiver cell type, ligands with positive Pearson correlation were filtered based on 1) either belonging to the list of top 20 ligands or having a Pearson correlation greater than 0.1, and 2) presence of the corresponding receptor in over 10% of cells (manually validated using CellPhoneDB [73]).
    CellPhoneDB
    suggested: (CellPhoneDB, RRID:SCR_017054)
    GO and TF analysis was conducted using the “EnrichR” package, and statistical significance was qualified using the EnrichR adjusted p-value based on Fisher’s exact test, with a significance threshold of p<0.05.
    EnrichR
    suggested: (Enrichr, RRID:SCR_001575)

    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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04324021TerminatedEfficacy and Safety of Emapalumab and Anakinra in Reducing H…

    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.
    • 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.

  4. Version published to 10.1101/2020.06.15.147470v1 on bioRxiv