In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

  1. Nicole A. P. Lieberman
  2. Vikas Peddu
  3. Hong Xie
  4. Lasata Shrestha
  5. Meei-Li Huang
  6. Megan C. Mears
  7. Maria N. Cajimat
  8. Dennis A. Bente
  9. Pei-Yong Shi
  10. Francesca Bovier
  11. Pavitra Roychoudhury
  12. Keith R. Jerome
  13. Anne Moscona
  14. Matteo Porotto
  15. Alexander L. Greninger

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Abstract

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  1. Version published to 10.1371/journal.pbio.3000849
  2. ScreenIT

    SciScore for 10.1101/2020.06.22.165225: (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.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Raw FASTQ files were adapter and quality trimmed by Trimmomatic v0.39 (54) using the call “leading 3 trailing 3 slidingwindow:4:15 minlen 20”.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Trimmed reads were pseudoaligned to the Ensembl v96 human transcriptome using Kallisto v0.46 (55) assuming an average library size of 300+/−100 base pairs.
    Ensembl
    suggested: (Ensembl, RRID:SCR_002344)
    Kallisto
    suggested: (kallisto, RRID:SCR_016582)
    Differential Expression: Pseudoaligned reads were pre-filtered to remove any genes with average expression of less than one read per sample, then normalized and differential expression calculated with the R package DEseq2 v1.28.1 (56).
    DEseq2
    suggested: (DESeq2, RRID:SCR_015687)
    Gene Set Enrichment Analysis (GSEA): GSEA was performed on normalized counts on GSEA Software version 4.0.3 (21,22)
    GSEA
    suggested: (SeqGSEA, RRID:SCR_005724)
    Metagenomics: Metagenomic analysis of the RNA sequence was performed using CLOMP v0.1.4 (17) with the default options and visualized using the Pavian metagenomic explorer (57).
    CLOMP
    suggested: None
    Viral species level taxonomical classifications with an RPM greater than 25 were confirmed via BLAST v2.10.1 (e-value 1e-5).
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Statistical enrichment tests of Gene Ontology (24,25) and DisGeNET (28) pathways were performed in the clusterProfiler R package (59).
    clusterProfiler
    suggested: (clusterProfiler, RRID:SCR_016884)
    Images were generated using packages including DOSE (60), ggplot2, pheatmap, and VennDiagram.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    VennDiagram
    suggested: (VennDiagram, RRID:SCR_002414)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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 10.1101/2020.06.22.165225v1 on bioRxiv