Structure and immune recognition of the porcine epidemic diarrhea virus spike protein

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1. 

   ScreenIT

   Jun 4, 2020

   SciScore for 10.1101/2020.02.18.955195: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   For both 293F and 293S cells, 1 L of cells at 1×106 cells were transfected with complexes composed of 250 μg of plasmid DNA and 750 μg of polyethylenimine (Polysciences, Cat. # 24765-1).	293S suggested: RRID:CVCL_A784)
   Mass spectrometry: The PEDV spike sample expressed in Sf9 cells was analyzed on Zorbax SB-C18 column (Agilent) with water with 0.1% formic acid and acetonitrile with 0.1% formic acid as mobile phases.	Sf9 suggested: None
   …

   SciScore for 10.1101/2020.02.18.955195: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   For both 293F and 293S cells, 1 L of cells at 1×106 cells were transfected with complexes composed of 250 μg of plasmid DNA and 750 μg of polyethylenimine (Polysciences, Cat. # 24765-1).	293S suggested: RRID:CVCL_A784)
   Mass spectrometry: The PEDV spike sample expressed in Sf9 cells was analyzed on Zorbax SB-C18 column (Agilent) with water with 0.1% formic acid and acetonitrile with 0.1% formic acid as mobile phases.	Sf9 suggested: None
   Software and Algorithms
   Sentences	Resources
   Briefly for spike samples, particles were extracted in RELION binning by 2 and then reconstructed in CryoSparc.	RELION suggested: (RELION, RRID:SCR_016274)
   Micrograph movies were aligned using MotionCor2 (UCSF) (Zheng et al., 2017), CTF corrections were done with Gctf (Zhang, 2016) and images were assessed with EMHP (Berndsen et al., 2017).	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   The model was aligned an mutated to the PEDV spike sequence and rebuild using Coot (Emsley et al., 2010).	Coot suggested: (Coot, RRID:SCR_014222)
   Model validation was done using Molprobity (Williams et al., 2018) and EMRinger (Barad et al., 2015).	Molprobity suggested: (MolProbity, RRID:SCR_014226)
   : Statistical models inherent to RELION-3.0 (Zivanov et al., 2018) and CryoSparc 2.0 (Punjani et al., 2017) were used to create 3D classifications and 3D refinements from spike particle images.	CryoSparc suggested: (cryoSPARC, RRID:SCR_016501)

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   Results from OddPub: Thank you for sharing your 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 17. 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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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 10.1101/2020.02.18.955195 on bioRxiv

   Feb 19, 2020