IL-13 is a driver of COVID-19 severity

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1. Version published to 10.1172/jci.insight.150107

   Jun 29, 2021
2. 

   Version published to 10.1101/2020.06.18.20134353v2 on medRxiv

   Mar 1, 2021
3. 

   ScreenIT

   Jun 21, 2020

   SciScore for 10.1101/2020.06.18.20134353: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The collection of biological specimens and de-identified patient information was approved by the University of Virginia Institutional Review Board (IRB-HSR #22231 and 200110). IACUC: In mice, neutralizing antibodies or isotype controls were used to assess the role of IL-13 during COVID-19 All mouse work was approved by the University of Virginia Institutional Animal Care and Use Committee, and all procedures were performed in the University certified animal Biosafety Level Three laboratory.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   SciScore for 10.1101/2020.06.18.20134353: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The collection of biological specimens and de-identified patient information was approved by the University of Virginia Institutional Review Board (IRB-HSR #22231 and 200110). IACUC: In mice, neutralizing antibodies or isotype controls were used to assess the role of IL-13 during COVID-19 All mouse work was approved by the University of Virginia Institutional Animal Care and Use Committee, and all procedures were performed in the University certified animal Biosafety Level Three laboratory.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   These P1 stocks were then used to infect additional Vero E6 cells, generating passage 2 (P2) stocks, which were used for all experiments.	Vero E6 suggested: RRID:CVCL_XD71)
   Software and Algorithms
   Sentences	Resources
   Drug use was identified via RxNorm codes for Dupilumab (1876376) and the lab value for C-reactive protein (9063).	RxNorm suggested: (RxNorm, RRID:SCR_006645)
   Library preparation, sequencing, quality control, and read mapping was performed by the Genome Analysis and Technology Core, RRID:SCR_018883.	by the detected: Virginia University School of Medicine Genome Analysis and Technology Core Facility ( RRID:SCR_018883)
   RNAseq data analysis: RNAseq reads were first processed using Cutadapt (Martin, 2011) to trim the adapter sequences and then the quality of the reads was assessed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (Ewels et al., 2016).	FastQC suggested: (FastQC, RRID:SCR_014583) MultiQC suggested: (MultiQC, RRID:SCR_014982)
   After these processes the reads were aligned to the mouse Ensembl GRCh38.76 primary assembly using STAR v2.5.3a (Dobin and Gingeras, 2015) in a two-passing mode to generate a gene matrix for differential gene expression.	STAR suggested: (STAR, RRID:SCR_015899)
   Differentially expressed genes were determined using the DESeq2 package (Love et al., 2014) in Rstudio (RStudio Team (2020).	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   For hierarchical clustering, the pheatmap function in the pheatmap library was used (R-project.org).	pheatmap suggested: (pheatmap, RRID:SCR_016418)
   Statistical analyses were performed using GraphPad Prism and R.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   ROC curve was generated using pROC library in RStudio.	RStudio suggested: (RStudio, RRID:SCR_000432)

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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
   NCT04640168	Recruiting	Adaptive COVID-19 Treatment Trial 4 (ACTT-4)

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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: We did not find any issues relating to colormaps.

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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 10.1101/2020.06.18.20134353v1 on medRxiv

   Jun 20, 2020