A thermostable, closed SARS-CoV-2 spike protein trimer

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1. Version published to 10.1038/s41594-020-0478-5

   Jul 31, 2020
2. 

   ScreenIT

   Jun 18, 2020

   SciScore for 10.1101/2020.06.15.152835: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethical approval was obtained from the East of England – Cambridge Central Research Ethics Committee (REC ref 17/EE/0025). Consent: All participants provided informed consent.
   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
   Presence of His-tagged protein was detected by chemical luminescence using His-probe (H-3) HRP (sc-8036 HRP, Santa Cruz Biotechnology) monoclonal antibody horseradish peroxidase (HRP) conjugate and Pierce™ ECL Western Blotting Substrate (Thermo Fisher)	sc-8036 HRP , Santa Cruz Biotechnology sug…

   SciScore for 10.1101/2020.06.15.152835: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethical approval was obtained from the East of England – Cambridge Central Research Ethics Committee (REC ref 17/EE/0025). Consent: All participants provided informed consent.
   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
   Presence of His-tagged protein was detected by chemical luminescence using His-probe (H-3) HRP (sc-8036 HRP, Santa Cruz Biotechnology) monoclonal antibody horseradish peroxidase (HRP) conjugate and Pierce™ ECL Western Blotting Substrate (Thermo Fisher)	sc-8036 HRP , Santa Cruz Biotechnology suggested: None
   Goat anti-human IgG secondary antibody-Peroxidase (Fc-specific, Sigma) prepared at 1:3000 in PBST was then added and plates were incubated for 1 h at room temperature.	Goat anti-human IgG secondary antibody-Peroxidase ( Fc-specific , Sigma ) suggested: None anti-human IgG secondary antibody-Peroxidase suggested: None
   Beads were incubated for 30 min with a PE-labeled anti–human IgG-Fc antibody (Leinco/Biotrend), washed as described above, and resuspended in 100 μl PBS/Tween.	anti–human IgG-Fc suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   GISAID accession no. EPI_ISL_402124) 1, covering the region from the end of signal peptide sequence (starting with QCVN) to the beginning of the transmembrane domain (ending with QYIK), was synthesised and codon optimised for HEK293 human cell expression.	HEK293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Protein Production and Purification: Expi293 cells (Thermo Fisher) cultured in Expi293 media (Thermo Fisher) were maintained at 37°C.	Expi293 suggested: RRID:CVCL_D615)
   Software and Algorithms
   Sentences	Resources
   In a first Schedule called preprocess, movies were motion-corrected and dose-weighted using RELION’s implementation of the MotionCor2 algorithm 36; the contrast transfer function (CTF) was estimated by CTFFIND-4.1.13 37; and particles were automatically picked by template matching using a structure of the S protein filtered to 20 Å resolution as a 3D reference.	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   Models were built and adjusted manually in Coot 40.	Coot suggested: (Coot, RRID:SCR_014222)
   The unmasked model-to-map FSC was calculated in PHENIX for the refined model against the full reconstruction to validate the confidence of the atomic model.	PHENIX suggested: (Phenix, RRID:SCR_014224)
   All data analyses were performed using Prism 8 version 8.4.2 (GraphPad).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   In addition, the dilution of sero-positive samples required to give a 50% maximum signal (EC50) against different spike protein constructs was determined using non-linear regression analysis in Prism 8 version 8.4.2.	Prism suggested: (PRISM, RRID:SCR_005375)

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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 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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3. 

   Version published to 10.1101/2020.06.15.152835v1 on bioRxiv

   Jun 17, 2020