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  1. SciScore for 10.1101/2022.05.16.492062: (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

    Experimental Models: Cell Lines
    SentencesResources
    Sequencing data analysis: The original RNA-seq and Ribo-seq data (Calu3 cells infected with SARS-COV-2 for 7h) were downloaded form Gene Expression Omnibus database (GEO) under accession number GSE149973[9], In brief, all raw sequencing data low quality reads and linker were removed using fastp[10].
    Calu3
    suggested: None
    2.2. Proteomic and RNC-seq expression data: Proteomic (quantitative technique: DIA, A549 cells infected with SARS-COV-2 for 24h) and RNC-seq (human HBE cell line) expression data were extracted from two independent studies supplementary materials, respectively[13,14]. 2.3.
    A549
    suggested: None
    Software and Algorithms
    SentencesResources
    Sequencing data analysis: The original RNA-seq and Ribo-seq data (Calu3 cells infected with SARS-COV-2 for 7h) were downloaded form Gene Expression Omnibus database (GEO) under accession number GSE149973[9], In brief, all raw sequencing data low quality reads and linker were removed using fastp[10].
    Gene Expression Omnibus
    suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
    Lineage assignment using Pangolin lineage command line tool v3.0 (https://github.com/cov-lineages/pangolin) with standard model[15]. 2.4. Ka/Ks and charge evolution analysis: Due to high closely related (identity ∼ 99%) of SARS-COV-2 genomes, we used MAFFT v7 as multiple sequence aligner[16].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    PyMol was used to calculate the surface electrostatic potential by Adaptive Poisson Boltzmann solver (APBS), the color scale range was set from −1.0 to 1.0 kT/Å.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)

    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:
    • 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.

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