Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets

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1. Version published to 10.15252/msb.202110260

   Oct 28, 2021
2. 

   Version published to 10.1101/2021.01.27.428543v2 on bioRxiv

   Aug 25, 2021
3. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.01.27.428543: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Genome-scale metabolic modeling of the remdesivir-treated Vero E6 cell samples and prediction of anti-SARS-CoV-2 metabolic targets in combination with remdesivir: As with the metabolic modeling of the other datasets on SARS-CoV-2 infection, iMAT (Shlomi et al. 2008) together with ACHR was used to compute the metabolic flux distribution for each of the experimental groups, using the median expression TPM values of each group as the input to iMAT.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   For Weingarten-Gabby et al. 2020, a nested design for DE was needed and …

   SciScore for 10.1101/2021.01.27.428543: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Genome-scale metabolic modeling of the remdesivir-treated Vero E6 cell samples and prediction of anti-SARS-CoV-2 metabolic targets in combination with remdesivir: As with the metabolic modeling of the other datasets on SARS-CoV-2 infection, iMAT (Shlomi et al. 2008) together with ACHR was used to compute the metabolic flux distribution for each of the experimental groups, using the median expression TPM values of each group as the input to iMAT.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   For Weingarten-Gabby et al. 2020, a nested design for DE was needed and DESeq2 failed to run properly, and limma-voom (Law et al. 2014) was used.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   For metabolic pathways (in Figure 1E), those under the category “Metabolism” from KEGG (Kanehisa et al. 2021) were used.	KEGG suggested: (KEGG, RRID:SCR_012773)
   Lists of experimentally validated drugs reported in different studies compiled by Kuleshov et al. 2020 were downloaded from https://maayanlab.cloud/covid19/, which are then mapped to the genes they inhibit using data from DrugBank v5.1.7 (Wishart et al. 2018).	DrugBank suggested: (DrugBank, RRID:SCR_002700)
   STAR (Dobin et al. 2013) was used to align the reads to reference genome of the African green monkey (Chlorocebus sabaeus, https://useast.ensembl.org/Chlorocebus_sabaeus/Info/Annotation), with the SARS-CoV-2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_045512) added to the reference genome.	STAR suggested: (STAR, RRID:SCR_015899)
   The R packages ggplot2 (Wickham 2016), ComplexHeatmap (Gu et al. 2016) and visNetwork (https://cran.r-project.org/web/packages/visNetwork/index.html) were used to create the visualizations.	ggplot2 suggested: (ggplot2, RRID:SCR_014601) ComplexHeatmap suggested: (ComplexHeatmap, RRID:SCR_017270)

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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 did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 27. 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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4. 

   Version published to 10.1101/2021.01.27.428543v1 on bioRxiv

   Jan 28, 2021