Identification of lectin receptors for conserved SARS‐CoV‐2 glycosylation sites

Version published to 10.15252/embj.2021108375

Aug 23, 2021

SciScore for 10.1101/2021.04.01.438087: (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
After washing for 3 times, 100 μl of 0.2 μg/ml HRP-conjugated goat anti-Mouse IgG (H+L) (Thermo Fisher Scientific, 31430) or goat anti-Human IgG (H+L) (Promega, W4031) antibodies were added for 30 min at room temperature.	W4031 suggested: (Promega Cat# W4031, RRID:AB_430835)
Interactions were visualized by the incubation of tetramethylrhodamine (TRITC) labelled secondary goat anti-mouse IgG antibodies (Fc specific; 1:1000 dilution in binding buffer; Life …

SciScore for 10.1101/2021.04.01.438087: (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
After washing for 3 times, 100 μl of 0.2 μg/ml HRP-conjugated goat anti-Mouse IgG (H+L) (Thermo Fisher Scientific, 31430) or goat anti-Human IgG (H+L) (Promega, W4031) antibodies were added for 30 min at room temperature.	W4031 suggested: (Promega Cat# W4031, RRID:AB_430835)
Interactions were visualized by the incubation of tetramethylrhodamine (TRITC) labelled secondary goat anti-mouse IgG antibodies (Fc specific; 1:1000 dilution in binding buffer; Life Technologies) and goat anti-Human IgG (Fc specific)-Cy3 (1:1000 dilution in binding buffer; Merck).	anti-mouse IgG suggested: None anti-Human IgG suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Briefly, the day before transfection, 293-F cells were diluted to 0.7×106 cells/ml in 30 ml FreestyleTM 293-F medium and grown at 120 rpm at 37°C with 8% CO2.	293-F suggested: None
Briefly, HEK293-6E cells were cultivated in FreeStyle F17 expression medium (Thermo Fisher Scientific, A1383502	HEK293-6E suggested: RRID:CVCL_HF20)
AFM measured Spike binding to Vero E6 cells: Vero E6 cells were grown on culture dishes using DMEM containing 10% FBS, 500 units/mL penicillin and 100 µg/mL streptomycin, at 37°C with 5% CO2.	Vero E6 suggested: RRID:CVCL_XD71)
Software and Algorithms
Sentences	Resources
Briefly, proteins with a C-type lectin-like/IPR001304 domain were downloaded from InterPro 66.0 and supplemented with proteins obtained in jackhmmer searches using the PF00059.20 lectin C-type domain definition versus the mouse-specific UniProt and Ensembl databases.	InterPro suggested: (InterPro, RRID:SCR_006695) Ensembl suggested: (Ensembl, RRID:SCR_002344)
The C-type lectin-like regions were extracted from the full-length proteins using the SMART CLECT domain definition with hmmersearch v3.1b2 and extended by 5 amino acids on both sides.	SMART suggested: (SMART, RRID:SCR_005026)
To reduce redundancy, principal isoforms were selected using appris 2016_10.v24.	appris suggested: (APPRIS, RRID:SCR_012019)
Data analysis was performed using the Gwyddion 2.55 software.	Gwyddion suggested: (Gwyddion, RRID:SCR_015583)
The quantification of fluorescence was done using ProScanArray Express software (Perkin Elmer) employing an adaptive circle quantification method from 50 μm (minimum spot diameter) to 300 μm (maximum spot diameter).	ProScanArray Express suggested: None
Average RFU (relative fluorescence unit) values with local background subtraction of four spots and standard deviation of the mean were recorded using Microsoft Excel and GraphPad Prism.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137) GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
The full model is available at the MolSSI / BioExcel COVID-19 Molecular Structure and Therapeutics Hub (https://covid.molssi.org//models/#spike-protein-in-complex-with-human-ace2-spike-spike-binding).	BioExcel suggested: None

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).

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:

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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Identification of lectin receptors for conserved SARS‐CoV‐2 glycosylation sites

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