Article activity feed

  1. SciScore for 10.1101/2022.06.01.494101: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Protein samples were resolved by SDS polyacrylamide gel electrophoresis and transferred onto a nitrocellulose membrane using Trans-Blot Turbo Transfer System (Bio-Rad, Hercules, CA), followed by blocking for 1 h with 5% nonfat milk in Tris-buffered saline-Tween 20 buffer and probing with antibodies against Strep Tag (SAB2702215, Sigma-Aldrich), γ-catenin (sc-514115, Santa Cruz Biotechnology) and GAPDH (A00084, GenScript) (Supplementary Table 6).
    γ-catenin
    suggested: (Immunological Sciences Cat# AB-90215, RRID:AB_2892157)
    sc-514115, Santa Cruz Biotechnology
    suggested: None
    GAPDH
    suggested: None
    The washed membranes were incubated with secondary antibody StarBright Blue 700 Goat anti-mouse IgG (Bio-rad).
    anti-mouse IgG
    suggested: None
    Coverslips were washed three times with PBS before secondary anti-mouse antibodies incubation (1:1000 dilution).
    anti-mouse
    suggested: None
    For staining, cells were resuspended in PBS 0.1% BSA 0.01% NaN3 containing the monoclonal antibody PE mouse anti-human CD54 (BD Pharmingen) or its isotype control at a concentration of 1/500.
    anti-human CD54
    suggested: None
    The primary anti-ZO-1 antibody (ref. 61-7300, Invitrogen) was diluted at 1:100 in PBS containing 1% BSA and incubated for 3 h at RT.
    anti-ZO-1
    suggested: (Innovative Research Cat# 61-7300, RRID:AB_138452)
    The secondary antibody (anti-rabbit IgG-FITC, ref. 9887, Sigma) was diluted 1:200 in PBS and incubated for 1 h at RT.
    anti-rabbit
    suggested: (Sigma-Aldrich Cat# F9887, RRID:AB_259816)
    anti-rabbit IgG-FITC
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Briefly, VSV-G pseudotyped ORF7a or ORF7b lentivirus was produced by co-transfection of HEK293T cells with the pLVX-ORF7a or pLVX-ORF7b plasmids, pCMV-Gag-Pol and pCMV-VSV-G using Lipofectamine 2000 Reagent (Thermo Fisher Scientific) as per manufacturer instructions.
    HEK293T
    suggested: None
    RNA isolation and sequencing: WT A549, A549-ORF7a and A549-ORF7b cells were seeded (3×10E5) in 6-well plates and lysed using RLT buffer for RNA isolation (RNeasy mini kit, Qiagen).
    A549-ORF7b
    suggested: None
    After 24 h incubation, A549 cells were labeled with calcein-AM.
    A549
    suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
    Recombinant DNA
    SentencesResources
    Lentivirus production, cell culture and transduction: ORF7a or ORF7b coding sequences (codon-optimized for mammalian expression) were cloned into pLVX-EF1α-IRES-Puro Cloning and Expression Lentivector (System Biosciences) to generate pseudotyped lentiviral particles encoding the ORF7a or ORF7b accessory proteins of SARS-CoV-2 (Wuhan-Hu-1 isolate) at the CNIC (Centro Nacional de Investigaciones Cardiovasculares) Viral Vector Unit (ViVU).
    pLVX-EF1α-IRES-Puro
    suggested: None
    Briefly, VSV-G pseudotyped ORF7a or ORF7b lentivirus was produced by co-transfection of HEK293T cells with the pLVX-ORF7a or pLVX-ORF7b plasmids, pCMV-Gag-Pol and pCMV-VSV-G using Lipofectamine 2000 Reagent (Thermo Fisher Scientific) as per manufacturer instructions.
    pLVX-ORF7a
    suggested: None
    pLVX-ORF7b
    suggested: None
    pCMV-Gag-Pol
    suggested: None
    pCMV-VSV-G
    suggested: RRID:Addgene_8454)
    Software and Algorithms
    SentencesResources
    Raw counts were transformed with the vst function in the DESeq2 package (Love et al., 2014) of the R software version 3.6.3 (R Core Team, 2020), and subsequent PCA was performed with the prcomp function.
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)
    Finally, the PCA graph was made with Graphad Prism software.
    Graphad Prism
    suggested: None
    All sequencing data sets are available in the NCBI BioProject database under accession number PRJNA841835.
    BioProject
    suggested: (NCBI BioProject, RRID:SCR_004801)
    Enrichment analyses were carried out by selecting the genomics sources: KEGG Pathway, GO Biological Processes, Reactome Gene Sets, Canonical Pathways, and CORUM.
    GO Biological
    suggested: None
    Relative expression results were calculated using GenEx6 Pro software (MultiD-Göteborg, Sweden), based on the Cq values obtained.
    GenEx6 Pro
    suggested: None
    For these experiments, a CytoFLEX flow cytometer (Beckman Coulter) was used and data was analyzed using FlowJo v10 (BD Biosciences).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)

    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.


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    Read the original source
    Was this evaluation helpful?