Endomembrane systems are reorganized by ORF3a and Membrane (M) of SARS-CoV-2

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   ScreenIT

   Jun 4, 2021

   SciScore for 10.1101/2021.06.01.446555: (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
   To detect expression pattern or biotinylation pattern, the primary antibody, such as anti-V5 (Invitrogen, cat. No. R960-25, 1:5,000 dilution), was incubated for 1 h at room temperature.	anti-V5 suggested: (Thermo Fisher Scientific Cat# R960-25, RRID:AB_2556564)
   After washing three times with TBST for 5 min at room temperature, secondary antibodies, namely mouse-HRP (Bio-rad, cat. No. 1706516, 1:3,000 dilution) and rabbit-HRP (Cell signaling, cat. No. 7074S, 1:3,000 dilution), or SA-HRP …

   SciScore for 10.1101/2021.06.01.446555: (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
   To detect expression pattern or biotinylation pattern, the primary antibody, such as anti-V5 (Invitrogen, cat. No. R960-25, 1:5,000 dilution), was incubated for 1 h at room temperature.	anti-V5 suggested: (Thermo Fisher Scientific Cat# R960-25, RRID:AB_2556564)
   After washing three times with TBST for 5 min at room temperature, secondary antibodies, namely mouse-HRP (Bio-rad, cat. No. 1706516, 1:3,000 dilution) and rabbit-HRP (Cell signaling, cat. No. 7074S, 1:3,000 dilution), or SA-HRP (Thermofisher, cat. No. 21126, 1:10,000 dilution) were incubated for 1 h at room temperature.	mouse-HRP suggested: None rabbit-HRP suggested: (Carl Roth Cat# 4750, RRID:AB_2890006)
   Experimental Models: Cell Lines
   Sentences	Resources
   HeLa cells and A549 cells were from Laboratory of Dr.	HeLa suggested: None A549 suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
   Obtaining Secreted Proteins in Cell Culture Media: After biotin labeling of HEK293 cells expressing SEC61B-TurboID, cells were incubated with no FBS DMEM for 16 h.	HEK293 suggested: None
   Proteome Digestion & Enrichment of Biotinylated Peptides: For mass sampling, HEK293T cells were split in three T75 flasks for triplicate samples per each condition.	HEK293T suggested: None
   Recombinant DNA
   Sentences	Resources
   Expression Plasmids: Genes with epitope tag (i.e. V5, FLAG, HA, twin strep) were cloned into pCDNA3, pCDNA3.1, and pCDNA5 using digestion with enzymatic restriction sites and ligation with T4 DNA ligase.	pCDNA3 suggested: RRID:Addgene_15475) pCDNA3.1 suggested: RRID:Addgene_79663) pCDNA5 suggested: RRID:Addgene_49428)
   For transiently co-expressed two constructs, vPOI-GFP and TurboID-GBP, cells were grown at 70–80% confluence and transfected with wanted constructs using PEI.	vPOI-GFP suggested: None
   Software and Algorithms
   Sentences	Resources
   Pearson correlation was conducted using image J software program (NIH).	image J suggested: (ImageJ, RRID:SCR_003070)
   After washing three times with TBST for 5 min at room temperature, results of immunoblotting assay were obtained using ECL solution using GENESYS program.	GENESYS suggested: (GeneSys, RRID:SCR_015770)
   Enlarged fluorescence images were fitted to the electron micrographs using the Image J BigWarp program.	Image J BigWarp suggested: None
   Processing MS data and Identification of Proteins: All MS/MS data were searched using MaxQuant (version 1.5.3.30) with Andromeda search engine at 10 ppm precursor ion mass tolerance against the SwissProt Homo sapiens proteome database (20,199 entries, UniProt (http://www.uniprot.org/)).	MaxQuant suggested: (MaxQuant, RRID:SCR_014485) UniProt suggested: (UniProtKB, RRID:SCR_004426)
   The imputation of protein intensity were conducted using Perseus software program.	Perseus suggested: (Perseus, RRID:SCR_015753)

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

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   Read the original source
2. 

   Version published to 10.1101/2021.06.01.446555v1 on bioRxiv

   Jun 1, 2021