Metabolic stress and disease-stage specific basigin expression of peripheral blood immune cell subsets in COVID-19 patients

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1. 

   ScreenIT

   Sep 21, 2020

   SciScore for 10.1101/2020.09.18.20194175: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The study was approved by the appropriate Institutional Review Board (University Hospital Regensburg, No. 20-1785-101) and conformed to the principles outlined in the Declaration of Helsinki.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Controls were asymptomatic healthy individuals with age median of 46.7 (IQR 37.25-46.7) and male sex in 47%.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody response was defined by presence of SARS-CoV-2 specific IgG antibodies in serum.	SARS-CoV-2 specific IgG suggested: None
   Cells were stained with surface antibodies as …

   SciScore for 10.1101/2020.09.18.20194175: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The study was approved by the appropriate Institutional Review Board (University Hospital Regensburg, No. 20-1785-101) and conformed to the principles outlined in the Declaration of Helsinki.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Controls were asymptomatic healthy individuals with age median of 46.7 (IQR 37.25-46.7) and male sex in 47%.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody response was defined by presence of SARS-CoV-2 specific IgG antibodies in serum.	SARS-CoV-2 specific IgG suggested: None
   Cells were stained with surface antibodies as described above and incubated in with 2-NBDG (45 min) or BODIPY 500/510 C1, C12 (20 min).	C12 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   SARS-CoV-2 infection of A549 cells was performed and published by Blanco-Melo et al (Blanco-Melo et al., 2020).	A549 suggested: None
   Software and Algorithms
   Sentences	Resources
   Tables of raw uniquely mapped read counts per human gene were generated during mapping using the built-in --quantMode GeneCounts option in STAR.	STAR suggested: (STAR, RRID:SCR_015899)
   Differential expression analysis was carried out on raw gene counts using edgeR 3.20.8 (Robinson et al., 2009) in R (3.4.3).	edgeR suggested: (edgeR, RRID:SCR_012802)
   Volcano plots were generated using the ggplot2 (v3.1.0) package in R.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   The rank-based gene set enrichment tests in Figure 5 were done using the fry function of the limma package (Ritchie et al., 2015) and plotted using the barcodeplot function in R.	limma suggested: (LIMMA, RRID:SCR_010943)
   Gene-sets were defined in the hallmark gene set collection (Liberzon et al., 2015) and basigin interaction partners were defined by STRING (Szklarczyk et al., 2019).	STRING suggested: (STRING, RRID:SCR_005223)
   Statistics: GraphPad Prism was used for statistical analyses, using ANOVA with post-hoc Bonferroni test and Mann-Whitney U test.	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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04275245	Recruiting	Clinical Study of Anti-CD147 Humanized Meplazumab for Inject…

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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 26. 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 10.1101/2020.09.18.20194175v2 on medRxiv

   Sep 19, 2020
3. 

   Version published to 10.1101/2020.09.18.20194175v1 on medRxiv

   Sep 18, 2020