SARS-CoV-2 infection causes transient olfactory dysfunction in mice

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   ScreenIT

   Nov 11, 2020

   SciScore for 10.1101/2020.11.10.376673: (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
   Sentences	Resources
   Multiplex antibody panels applied in this study were: hACE2 (Abcam, ab108209, 1:200); tdTomato (Rockland, 600-401-379, 1:500); SARS-CoV-2 nucleocapsid protein (Sinobiological, 40143-R004, 1:1000);	SARS-CoV-2 nucleocapsid protein ( Sinobiological , 40143-R004 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell and Virus: The Vero cells were maintained at 37℃ under 5% CO2 in Dulbecco’s modified Eagle essential medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 10 mM HEPES and 1% penicillin/streptomycin.	Vero suggested: None
   Software and Algorithms
   Sentences	Re…

   SciScore for 10.1101/2020.11.10.376673: (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
   Sentences	Resources
   Multiplex antibody panels applied in this study were: hACE2 (Abcam, ab108209, 1:200); tdTomato (Rockland, 600-401-379, 1:500); SARS-CoV-2 nucleocapsid protein (Sinobiological, 40143-R004, 1:1000);	SARS-CoV-2 nucleocapsid protein ( Sinobiological , 40143-R004 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell and Virus: The Vero cells were maintained at 37℃ under 5% CO2 in Dulbecco’s modified Eagle essential medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 10 mM HEPES and 1% penicillin/streptomycin.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   Clean reads were aligned to the mouse genome (Mus_musculus.GRCm38.99) using Hisat2 v2.1.0.	Hisat2 suggested: (HISAT2, RRID:SCR_015530)
   The number of reads mapped to each gene in each sample was counted by HTSeq v0.6.0 and TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was then calculated to estimate the expression level of genes in each sample.	HTSeq suggested: (HTSeq, RRID:SCR_005514)
   Database search: The raw files from OE and OB groups were searched with MaxQuant (v1.5.5.0) against the mouse reviewed proteome downloaded from UniProt containing 17,478 entries and a canonical SARS-CoV-2 proteome with 30 potentially viral proteins from the SARS-CoV-2 genome (NC_045512.2), and a common contaminant database (http://www.maxquant.org/contaminants.zip), respectively.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485) UniProt suggested: (UniProtKB, RRID:SCR_004426)
   Bioinformatic analyses: DESeq2 v1.6.3 was used for differential gene expression analysis.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   DEGs and DEPs were used as query to search for enriched biological processes (Gene ontology BP) using Metascape (Zhou et al., 2019)	Metascape suggested: (Metascape, RRID:SCR_016620)
   KEGG pathway enrichment and protein interaction network were analyzed using STRING (Szklarczyk et al., 2019).	KEGG suggested: (KEGG, RRID:SCR_012773) STRING suggested: (STRING, RRID:SCR_005223)
   Heatmaps of gene expression levels were constructed using pheatmap package in R (https://cran.rstudio.com/web/packages/pheatmap/index.html).	pheatmap suggested: (pheatmap, RRID:SCR_016418)
   Dot plots and volcano plots were constructed using ggplot2 (https://ggplot2.tidyverse.org/) package in R.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Statistical analysis: Data were analyzed using GraphPad Prism 8 (GraphPad Software, San Diego, California, USA).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   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).

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24 and 25. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   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.

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2. 

   Version published to 10.1101/2020.11.10.376673v1 on bioRxiv

   Nov 10, 2020