Quantitative proteomics of hamster lung tissues infected with SARS‐CoV‐2 reveal host factors having implication in the disease pathogenesis and severity

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1. Version published to 10.1096/fj.202100431r

   Jun 9, 2021
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   ScreenIT

   Mar 15, 2021

   SciScore for 10.1101/2021.03.09.434371: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All the experiments were done with prior approval of Institutional Biosafety Committee (IBSC) and Institutional Animal Ethical Committee (IAEC).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Horse serum (Vector Laboratories) was used for blocking the sections for 30 min at room temperature and incubated with Ki-67 antibody (#VP-RM04; Vector Laboratories, 1:100) overnight at 4°C.	Ki-67 suggested: None #VP-RM04 suggested: (Vector Laboratories Cat# VP-RM04, RRID:AB_2336545)
   Sections were washed twice with 1x PBS and treated with biotinylated …

   SciScore for 10.1101/2021.03.09.434371: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All the experiments were done with prior approval of Institutional Biosafety Committee (IBSC) and Institutional Animal Ethical Committee (IAEC).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Horse serum (Vector Laboratories) was used for blocking the sections for 30 min at room temperature and incubated with Ki-67 antibody (#VP-RM04; Vector Laboratories, 1:100) overnight at 4°C.	Ki-67 suggested: None #VP-RM04 suggested: (Vector Laboratories Cat# VP-RM04, RRID:AB_2336545)
   Sections were washed twice with 1x PBS and treated with biotinylated anti-rabbit/mouse IgG secondary antibody (Vector Laboratories) for 45 minutes, followed by ABC reagent for 30 min.	anti-rabbit/mouse IgG suggested: None
   The whole-cell lysates (WCL) were subjected to SDS-PAGE and transferred to nitrocellulose membrane (Thermo Scientific), followed by blocking and immunoblotting with antibodies specific for SARS-CoV-2 Nucleocapsid protein (#11-2003, Abgenex) or β-actin (#4970, CST) [15]. qRT-PCR: RNA isolation from culture supernatant was performed using QIAamp Viral RNA Mini Kit (#52906, Qiagen), and for hamster tissue samples, TRizol reagent (#10296010, Invitrogen) was used.	SARS-CoV-2 Nucleocapsid protein (#11-2003, Abgenex) suggested: None β-actin suggested: None
   Software and Algorithms
   Sentences	Resources
   Bioinformatics and statistical analysis: The Proteome Discoverer 2.3 (Thermo Scientific, Bremen, Germany) was used to carry out protein identification and quantitation.	Proteome Discoverer suggested: (Proteome Discoverer, RRID:SCR_014477)
   Gene Ontology (GO) and pathway analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed using the EnrichR online tool http://amp.pharm.mssm.edu/Enrichr/) [19].	KEGG suggested: (KEGG, RRID:SCR_012773) EnrichR suggested: (Enrichr, RRID:SCR_001575)
   Data availability: The raw data files and the MSF files were submitted to the PRIDE partner repository [20] with dataset identifier PXD024547.	PRIDE suggested: (Pride-asap, RRID:SCR_012052)

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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 did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 27. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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 10.1101/2021.03.09.434371v1 on bioRxiv

   Mar 9, 2021