SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

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1. Version published to 10.1038/s41594-020-0511-8

   Sep 9, 2020
2. 

   ScreenIT

   Jul 7, 2020

   SciScore for 10.1101/2020.07.07.191676: (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

   Antibodies
   Sentences	Resources
   Fractions were precipitated with trichloroacetic acid (TCA) and subjected to Western blot analysis (anti-His antibody, Clontech).	anti-His suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Preparation of viral 5’-UTR mRNA and reporter RLuc mRNA: Preparation of HeLa translation-competent lysates: HeLa S3 lysates were prepared similarly as described before15.	HeLa suggested: None
   For this, frozen HEK293E cells were thawed and resuspended in 2x …

   SciScore for 10.1101/2020.07.07.191676: (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

   Antibodies
   Sentences	Resources
   Fractions were precipitated with trichloroacetic acid (TCA) and subjected to Western blot analysis (anti-His antibody, Clontech).	anti-His suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Preparation of viral 5’-UTR mRNA and reporter RLuc mRNA: Preparation of HeLa translation-competent lysates: HeLa S3 lysates were prepared similarly as described before15.	HeLa suggested: None
   For this, frozen HEK293E cells were thawed and resuspended in 2x excess of lysis buffer (25 mM HEPES-KOH pH 7.6, 5 mM MgCl2, 50 mM KCl, cOmplete protease inhibitor cocktail (Roche), 1 mM PMSF, 0.2 U/µl RiboLock).	HEK293E suggested: None
   Micrographs (10’104 for the in vitro binding experiment, 16’887 for the HEK cell extract) were carefully inspected based on CTF estimations for drift and ice quality.	HEK suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Software and Algorithms
   Sentences	Resources
   The plate was incubated at 30 °C for 10 min and the luminescence signal was measured three times using the TECAN infinite M100 Pro plate reader and plotted on GraphPad after performing three independent biological replicates.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The super-resolution micrographs collected with the K3 camera were additionally binned 2 times during the MotionCor2 procedure.	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   Zenodo https://doi.org/10.5281/zenodo.3576630 (2019)).	Zenodo suggested: (ZENODO, RRID:SCR_004129)
   The coordinates were subjected to 5 cycles of real space refinement using PHENIX 1.1827.	PHENIX suggested: (Phenix, RRID:SCR_014224)

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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 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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3. 

   Version published to 10.1101/2020.07.07.191676v1 on bioRxiv

   Jul 7, 2020