Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium

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1. Version published to 10.1172/jci140766

   Jan 4, 2021
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.22.111187: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Subjects and samples: For the use of human tissue for research, all studies were approved by the Vanderbilt Institutional Review Board (VanderbiltIRB #’s 060165, 171657, 200490). IACUC: Animal care: The protocol for this was approved by the Institutional Animal Care and Use Committee of Vanderbilt University (Nashville, TN) and was in compliance with the Public Health Services policy on humane care and use of laboratory animals.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Adult tissue included male and female donors, and all were lifetime nonsmokers.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After …

   SciScore for 10.1101/2020.05.22.111187: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Subjects and samples: For the use of human tissue for research, all studies were approved by the Vanderbilt Institutional Review Board (VanderbiltIRB #’s 060165, 171657, 200490). IACUC: Animal care: The protocol for this was approved by the Institutional Animal Care and Use Committee of Vanderbilt University (Nashville, TN) and was in compliance with the Public Health Services policy on humane care and use of laboratory animals.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Adult tissue included male and female donors, and all were lifetime nonsmokers.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After 2% FBS staining buffer wash, cells were incubated with the conjugated primary antibodies anti-CD45 (BD cat # 559864) and anti-Ter119 (BD cat# 116211) as indicated below.	anti-CD45 suggested: (BD Biosciences Cat# 559864, RRID:AB_398672) anti-Ter119 suggested: (STEMCELL Technologies Cat# 60033, RRID:AB_2783004)
   We used a monoclonal antibody to TMRPSS2 (Abcam, ab109131) and RNAScope probes to TMPRSS2 and FOXJ1 in human samples and Tmprss2 and Foxj1 in murine samples.	TMRPSS2 suggested: None TMPRSS2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Detailed Methods Figures S1–9 Animal Care and Tissue Fixation: C57BL/6 mice were used for all experiments.	C57BL/6 suggested: None
   RNAScope probes to the following human genes were used: TMPRSS2, ACE2, SCGB1A1,	TMPRSS2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Data availability: Raw data and counts matrices used in generating this dataset are available through the Gene Expression Omnibus (GEO) (pending).	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   Ambient RNA filtering: Ambient background RNA were cleaned from the scRNA-seq data with “SoupX” (version 1.2.2, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK); (2)) in RStudio (version 1.2.5001, RStudio, Inc., Boston, Massachusetts,	RStudio suggested: (RStudio, RRID:SCR_000432)

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   Results from OddPub: Thank you for sharing your code and data.

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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 8. 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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3. 

   Version published to 10.1101/2020.05.22.111187 on bioRxiv

   May 23, 2020