Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

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1. 

   ScreenIT

   Jun 4, 2020

   SciScore for 10.1101/2020.02.19.956581: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All experiments were conducted at the Fred Hutchinson Cancer Research Center according to approved Institutional Animal Care and Use Committee protocols.
   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

   Antibodies
   Sentences	Resources
   An anti-S2 SARS-CoV S monoclonal primary antibody (1:150 dilution) or an MLV p30 monoclonal antibody (1:1,000 dilution, AbCam) and an Alexa Fluor 680-conjugated goat anti-human or mouse secondary antibody (1:30,000 and 1:15,000 dilution respectively, Jackson Laboratory) were used for Western-blotting.	anti-S2 …

   SciScore for 10.1101/2020.02.19.956581: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All experiments were conducted at the Fred Hutchinson Cancer Research Center according to approved Institutional Animal Care and Use Committee protocols.
   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

   Antibodies
   Sentences	Resources
   An anti-S2 SARS-CoV S monoclonal primary antibody (1:150 dilution) or an MLV p30 monoclonal antibody (1:1,000 dilution, AbCam) and an Alexa Fluor 680-conjugated goat anti-human or mouse secondary antibody (1:30,000 and 1:15,000 dilution respectively, Jackson Laboratory) were used for Western-blotting.	anti-S2 SARS-CoV suggested: None anti-human suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Both constructs were produced in 500mL HEK293F cells grown in suspension using FreeStyle 293 expression medium (Life technologies) at 37°C in a humidified 8% CO2 incubator rotating at 130 rpm.	HEK293F suggested: None
   HEK293T cells were cotransfected using Lipofectamine 2000 (Life Technologies) with an S encoding-plasmid, an MLV Gag-Pol packaging construct and the MLV transfer vector encoding a luciferase reporter, according to the manufacturer’s instructions.	HEK293T suggested: None
   Pseudovirus entry assays: VeroE6 and Baby Hamster Kidney (BHK) cells were cultured in 10% FBS, 1% PenStrep DMEM. BHK or VeroE6 cells were plated into 12 well plates at a density of 0.3 x 106 for 16 hours.	BHK suggested: None VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Software and Algorithms
   Sentences	Resources
   For each data set two rounds of reference-free 2D classification were performed using cryoSPARC (Punjani et al., 2017) to select well-defined particle images.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   CryoEM model building and analysis: UCSF Chimera (Goddard et al., 2007) and Coot were used to fit atomic models (PDB 6NB6) into the cryoEM map.	Coot suggested: (Coot, RRID:SCR_014222)
   Models were analyzed using MolProbity (Chen et al., 2010) and privateer (Agirre et al., 2015).	MolProbity suggested: (MolProbity, RRID:SCR_014226)

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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: 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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   Read the original source
2. Version published to 10.1016/j.cell.2020.02.058

   Apr 1, 2020
3. 

   Version published to 10.1101/2020.02.19.956581v1 on bioRxiv

   Feb 20, 2020