A universal bacteriophage T4 nanoparticle platform to design multiplex SARS-CoV-2 vaccine candidates by CRISPR engineering

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1. Version published to 10.1126/sciadv.abh1547

   Sep 10, 2021
2. 

   ScreenIT

   Jan 21, 2021

   SciScore for 10.1101/2021.01.19.427310: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All mouse experiments were approved by the Institutional Animal Care and Use Committee of the Catholic University of America (Washington, DC) (Office of Laboratory Animal Welfare assurance number A4431-01) and the University of Texas Medical Branch (Galveston, TX) (Office of Laboratory Animal Welfare assurance number A3314-01).
   Randomization	Six- to eight-week-old female BALB/c mice (The Jackson Laboratory) were randomly grouped (5 mice per group) and allowed to acclimate for 14 days.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Six- to eight-week-old female BALB/c mice (The Jackson Laboratory) were randomly grouped (5 mice per …

   SciScore for 10.1101/2021.01.19.427310: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All mouse experiments were approved by the Institutional Animal Care and Use Committee of the Catholic University of America (Washington, DC) (Office of Laboratory Animal Welfare assurance number A4431-01) and the University of Texas Medical Branch (Galveston, TX) (Office of Laboratory Animal Welfare assurance number A3314-01).
   Randomization	Six- to eight-week-old female BALB/c mice (The Jackson Laboratory) were randomly grouped (5 mice per group) and allowed to acclimate for 14 days.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Six- to eight-week-old female BALB/c mice (The Jackson Laboratory) were randomly grouped (5 mice per group) and allowed to acclimate for 14 days.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Anti-NP or anti-RBD primary antibodies were added to the blots and incubated overnight at 4°C in PBS-5% BSA, followed by five times rinsing in PBST buffer [1×PBS (pH 7.4) and 0.05% Tween 20].	Anti-NP suggested: None anti-RBD suggested: None
   Goat-anti-mouse or goat-anti-rabbit HRP-conjugated antibody (Thermo Fisher) was applied at a 1:5000 dilution in 5% BSA-PBST for 1 hr at RT with gentle shaking.	Goat-anti-mouse suggested: (Electron Microscopy Sciences Cat# 815.022, RRID:AB_2629849) HRP-conjugated antibody suggested: None
   After rinsing five times in PBST for 5 min each, Alexa488- or Rhodamine-conjugated goat anti-human secondary antibody was added (1/500 dilution) (Thermo Fisher), and incubated for 2~3 hr at room temperature in the dark.	anti-human secondary suggested: None
   After washing five times with PBST (PBS + 0.05% Tween-20), the secondary antibody was added at 1:10,000 dilution in PBS–1% BSA buffer (100 μl per well) using either goat-anti-mouse IgG-HRP, goat-anti-mouse IgG1-HRP, goat-anti-mouse IgG2a-HRP (Thermo Fisher), or goat-anti-rabbit IgG-HRP (Abcam).	IgG-HRP suggested: None IgG1-HRP suggested: None IgG2a-HRP suggested: None IgG-HRP ( Abcam) . suggested: None
   Neutralizing antibody titers (expressed as IC50 or IC90) were obtained from four-parameter logistic curve-fits of cell death profiles using OriginPro 9 (Origin Lab Corp., Northampton, MA).	IC90 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The T4-SpyCatcher-GFP or T4-S trimer-GFP phages were resuspended in Opti-MEM medium (Thermo Fisher) and then added to ACE2-transfected HEK293T cells.	HEK293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   After incubation under BSL-3 conditions, 100 μl of the mixtures in individual wells were transferred to Vero E6 cell monolayer grown in 96-well microtiter plates that containing 100 μl of MEM/2%FCS medium in each well and were cultured for 72 h at 37°C before assessing the presence or absence of cytopathic effect (CPE)	Vero E6 suggested: None
   After preincubating the plates for 1 hr, 20 μl of Vero cells (106/ml), containing 50 μg/mL of propidium iodide (PI), was added to all wells using the liquid handler.	Vero suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Six- to eight-week-old female BALB/c mice (The Jackson Laboratory) were randomly grouped (5 mice per group) and allowed to acclimate for 14 days.	BALB/c suggested: None
   Software and Algorithms
   Sentences	Resources
   After Coomassie Blue R-250 (Bio-Rad, CA) staining and destaining, the protein bands on SDS-PAGE gels were scanned and quantified by ChemiDoc MP imaging system (BioRad) and image J.	image J suggested: (ImageJ, RRID:SCR_003070)
   Neutralizing antibody titers (expressed as IC50 or IC90) were obtained from four-parameter logistic curve-fits of cell death profiles using OriginPro 9 (Origin Lab Corp., Northampton, MA).	OriginPro suggested: None

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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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3. 

   Version published to 10.1101/2021.01.19.427310 on bioRxiv

   Jan 20, 2021