Structure and Immune Recognition of the Porcine Epidemic Diarrhea Virus Spike Protein
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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). 293Ssuggested: 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. Sf9suggested: 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). 293Ssuggested: 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. Sf9suggested: NoneSoftware and Algorithms Sentences Resources Briefly for spike samples, particles were extracted in RELION binning by 2 and then reconstructed in CryoSparc. RELIONsuggested: (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). MotionCor2suggested: (MotionCor2, RRID:SCR_016499)The model was aligned an mutated to the PEDV spike sequence and rebuild using Coot (Emsley et al., 2010). Cootsuggested: (Coot, RRID:SCR_014222)Model validation was done using Molprobity (Williams et al., 2018) and EMRinger (Barad et al., 2015). Molprobitysuggested: (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. CryoSparcsuggested: (cryoSPARC, RRID:SCR_016501)Results from OddPub: Thank you for sharing your data.
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
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.
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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