SARS-CoV-2 activates ER stress and Unfolded protein response

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   ScreenIT

   Jul 1, 2021

   SciScore for 10.1101/2021.06.21.449284: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Monoclonal anti-alpha-tubulin clone B-5-1-2 antibody (T5168, Sigma-Aldrich) was used as the loading control.	anti-alpha-tubulin suggested: (Sigma-Aldrich Cat# T5168, RRID:AB_477579)
   For phospho-protein quantification, the membranes were stripped, blocked and reprobed using a solution containing the corresponding anti-fosfospecific antibody.	anti-fosfospecific suggested: None
   Phosphorylated proteins densitometry values were divided by the total protein values and the α-tubulin antibody was used as the normalizer of the amount of proteins applied in the gel.	α-tubulin suggested: None
   …

   SciScore for 10.1101/2021.06.21.449284: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Monoclonal anti-alpha-tubulin clone B-5-1-2 antibody (T5168, Sigma-Aldrich) was used as the loading control.	anti-alpha-tubulin suggested: (Sigma-Aldrich Cat# T5168, RRID:AB_477579)
   For phospho-protein quantification, the membranes were stripped, blocked and reprobed using a solution containing the corresponding anti-fosfospecific antibody.	anti-fosfospecific suggested: None
   Phosphorylated proteins densitometry values were divided by the total protein values and the α-tubulin antibody was used as the normalizer of the amount of proteins applied in the gel.	α-tubulin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines, SARS-CoV-2 and infection assays: Vero cell line (ATCC CCL-81) were maintained in DMEM medium supplemented with 10% (v/v	Vero suggested: None
   (GenBank accession number MT126808) 20 was used to infect Vero CCL-81 and Calu-3 cells with multiplicity of infection (MOI) of 0.02.	Calu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   Software and Algorithms
   Sentences	Resources
   Graphics and SEM were done using GraphPad Prism software version 8.1	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   GraphPad Software, San Diego, USA).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository 28	PRIDE suggested: (Pride-asap, RRID:SCR_012052)
   Database Search and Statistical Analysis: Raw data were searched using Proteome Discoverer computational platform v2.3.0.523 (PD) using the Sequest search engine.	Proteome Discoverer suggested: (Proteome Discoverer, RRID:SCR_014477)
   Bioinformatics analysis: Gene ontology (GO) was performed using the g: profiler tool and GOplot package 30, available in Bioconductor.	GOplot suggested: None Bioconductor suggested: (Bioconductor, RRID:SCR_006442)
   Enriched pathways were determined by Reactome and KEGG platform (q-value < 0.05)32; complementary analyses were performed using the ReactomeFIPlugIn app 31.	KEGG suggested: (KEGG, RRID:SCR_012773)
   Complementary analyses were performed using Perseus,	Perseus suggested: (Perseus, RRID:SCR_015753)
   ggplot2 package, Graphpad prism v.8, and RStudio software.	ggplot2 suggested: (ggplot2, RRID:SCR_014601) RStudio suggested: (RStudio, RRID:SCR_000432)
   Peptides identified through MS data analysis were searched in the protein to better visualize their regions using PyMOL 2.4.1 Western blotting: Cells were lysed in SDC buffer containing protease (Roche, Basel, Switzerland) and phosphatase (Sigma-Aldrich) inhibitor cocktails.	PyMOL suggested: (PyMOL, RRID:SCR_000305)
   The volume density of the chemiluminescent bands was calculated as integrated optical density × mm2 using ImageJ Fiji.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   RNA-seq data reanalysis: The fastq files were downloaded from the https://sra-explorer.info/ platform with the BioProject accession number PRJNA646224 37 and processed on the Galaxy server 38.	BioProject suggested: (NCBI BioProject, RRID:SCR_004801)
   The ‘FastQC’ module was used to report the quality reads, following by the trimmed using Trim Galore (v. 0.4.3.1) set to the single-end library.	Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   The Trim Galore output sequences were aligned to the human reference genome hg38 using the HISAT2 (Galaxy Version 2.1.0+galaxy7	Galaxy suggested: (Galaxy, RRID:SCR_006281)
   The differently regulated genes were analyzed by the limma, Glimma, edgeR, and Homo.sapiens packages applying a cut-off of |log2FC|>1 and a p-adjusted value <0.05 (Benjamini-Hochberg).	limma suggested: (LIMMA, RRID:SCR_010943) Glimma suggested: (Glimma, RRID:SCR_017389) edgeR suggested: (edgeR, RRID:SCR_012802)

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

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   Read the original source
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   Version published to 10.1101/2021.06.21.449284v1 on bioRxiv

   Jun 21, 2021