A single-cell atlas of the peripheral immune response in patients with severe COVID-19

  1. Aaron J. Wilk
  2. Arjun Rustagi
  3. Nancy Q. Zhao
  4. Jonasel Roque
  5. Giovanny J. Martínez-Colón
  6. Julia L. McKechnie
  7. Geoffrey T. Ivison
  8. Thanmayi Ranganath
  9. Rosemary Vergara
  10. Taylor Hollis
  11. Laura J. Simpson
  12. Philip Grant
  13. Aruna Subramanian
  14. Angela J. Rogers
  15. Catherine A. Blish

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Abstract

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  1. Version published to 10.1038/s41591-020-0944-y
  2. ScreenIT

    SciScore for 10.1101/2020.04.17.20069930: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Subjects and specimen collection: We collected blood from 7 patients enrolled in the Stanford University ICU Biobank study from March-April 2020 after written informed consent from patients or their surrogates (Stanford IRB approval #28205).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Next, reads were aligned with STAR using the GRCh37 (hg19) human reference genome that included the complete genome sequences for all SARS-CoV-2 strains sequenced from California before March 24, 2020 (10 SARS-CoV-2 sequences).
    STAR
    suggested: (STAR, RRID:SCR_015899)
    Gene pathway and upstream regulator analysis was performed with Ingenuity Pathway Analysis (IPA; Qiagen).
    Ingenuity Pathway Analysis
    suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)

    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:
    • 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.

  3. Version published to 10.1101/2020.04.17.20069930 on medRxiv