Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

Version published to 10.1016/j.celrep.2022.111009

Jun 1, 2022

SciScore for 10.1101/2022.04.07.487528: (What is this?)

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

Table 1: Rigor

Ethics	not detected.
Sex as a biological variable	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Antibodies were incubated at room temperature for 1 hour, washed and binding detected with goat anti-human-HRP (Jackson ImmunoResearch Laboratories, PA) and TMB substrate.	anti-human-HRP suggested: None
Mouse anti-monkey IgG-HRP (Southern Biotech, CAT# 4700-05) and Goat anti-human IgG-HRP (Jackson ImmunoResearch Laboratories, CAT# 109-035-098) secondary antibodies were used to detect antibody bound to the spike proteins.	anti-monkey IgG-HRP suggested: (SouthernBiotech Cat# 4700-05, RRID:AB_…

SciScore for 10.1101/2022.04.07.487528: (What is this?)

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

Table 1: Rigor

Ethics	not detected.
Sex as a biological variable	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Antibodies were incubated at room temperature for 1 hour, washed and binding detected with goat anti-human-HRP (Jackson ImmunoResearch Laboratories, PA) and TMB substrate.	anti-human-HRP suggested: None
Mouse anti-monkey IgG-HRP (Southern Biotech, CAT# 4700-05) and Goat anti-human IgG-HRP (Jackson ImmunoResearch Laboratories, CAT# 109-035-098) secondary antibodies were used to detect antibody bound to the spike proteins.	anti-monkey IgG-HRP suggested: (SouthernBiotech Cat# 4700-05, RRID:AB_2796069) anti-human IgG-HRP suggested: None
RBD binding to IgG’s was assessed using a Series S CM5 chip (Cytiva, MA) which was labeled with anti-human IgG (fc) antibody using a Human Antibody Capture Kit (Cytiva, MA).	anti-human IgG suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Antibodies were produced in Expi293 cells (embryonal, human kidney).	Expi293 suggested: RRID:CVCL_D615)
293T/ACE2-MF cells were detached from T75 culture flasks using TrypLE Select Enzyme solution, suspended in growth medium (100,000 cells/ml) and immediately added to all wells (10,000 cells in 100 µL of growth medium per well).	293T/ACE2-MF suggested: None
Recombinant DNA
Sentences	Resources
The sequence was codon optimized for mammalian expression and subcloned into the pCAGGS mammalian expression vector under the AG promoter.	pCAGGS suggested: RRID:Addgene_127347)
Software and Algorithms
Sentences	Resources
https://www.addgene.org).	https://www.addgene.org suggested: (Addgene, RRID:SCR_002037)
Sensogram data were analyzed using the BiaEvaluation software (Cytiva, MA)	BiaEvaluation suggested: (BIAevaluation Software, RRID:SCR_015936)
The cryoSPARC (Punjani et al., 2017) software was used for data processing.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
Coot (Emsley et al., 2010)	Coot suggested: (Coot, RRID:SCR_014222)
, Pymol (Schrodinger, 2015), Chimera (Pettersen et al., 2004), ChimeraX (Goddard et al., 2018) and Isolde (Croll, 2018) were used for model building and refinement.	Pymol suggested: (PyMOL, RRID:SCR_000305)
Difference distance matrices (DDM): DDM were generated using the Bio3D package (Grant et al., 2020) implemented in R (R Core Team (2014).	Bio3D suggested: None

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: We did not find any issues relating to colormaps.

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.

Results from scite Reference Check: We found no unreliable references.

Read the original source

Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

This article has been Reviewed by the following groups

Listed in

Abstract

Article activity feed