Cell-Type-Specific Immune Dysregulation in Severely Ill COVID-19 Patients

  1. Changfu Yao
  2. Stephanie A. Bora
  3. Tanyalak Parimon
  4. Tanzira Zaman
  5. Oren A. Friedman
  6. Joseph A. Palatinus
  7. Nirmala S. Surapaneni
  8. Yuri P. Matusov
  9. Giuliana Cerro Chiang
  10. Alexander G. Kassar
  11. Nayan Patel
  12. Chelsi E.R. Green
  13. Adam W. Aziz
  14. Harshpreet Suri
  15. Jo Suda
  16. Andres A. Lopez
  17. Gislâine A. Martins
  18. Barry R. Stripp
  19. Sina A. Gharib
  20. Helen S. Goodridge
  21. Peter Chen

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Abstract

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  1. Version published to 10.1016/j.celrep.2020.108590
  2. ScreenIT

    SciScore for 10.1101/2020.07.23.20161182: (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

    Antibodies
    SentencesResources
    Totalseq-A human hashing antibodies (Biolegend) were used to label FACS sorted cells.
    Totalseq-A human hashing antibodies ( Biolegend )
    suggested: None
    Software and Algorithms
    SentencesResources
    Alignment, Demultiplexing, Quality Control and Batch Correction: CellRanger v3.0.0 software was used with the default settings for demultiplexing, aligning reads with STAR software to a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation with SARS-Cov2 virus genome MT246667.1, https://www.ncbi.nlm.nih.gov/nuccore/MT246667.1.
    STAR
    suggested: (STAR, RRID:SCR_015899)
    http://www.gencodegenes.org
    suggested: (HapMap 3 and ENCODE 3, RRID:SCR_004563)
    GENCODE
    suggested: (GENCODE, RRID:SCR_014966)
    In order to complement our GO analysis, we also performed canonical pathway analysis on all major immune cell types using Ingenuity Pathway Analysis (IPA)
    Ingenuity Pathway Analysis
    suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)
    Pathway module scores were calculated using the AddModuleScore function of the Seurat package that calculated the average expression of each gene signature list and subtracted by the aggregated expression of control feature sets.
    Seurat
    suggested: (SEURAT, RRID:SCR_007322)

    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 10.1101/2020.07.23.20161182 on medRxiv