Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2

  1. Harlan Barker
  2. Seppo Parkkila

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1371/journal.pone.0240647
  2. ScreenIT

    SciScore for 10.1101/2020.04.13.038752: (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
    SentencesResources
    According to Protein Expression Atlas the immunostainings were performed with the rabbit anti-human polyclonal antibody (HPA000288; Sigma Aldrich, St. Louis, MO) raised against 111 N-terminal amino acids of ACE2 and diluted 1:250 for the staining.
    anti-human polyclonal antibody
    suggested: None
    Software and Algorithms
    SentencesResources
    ] Python libraries.
    Python
    suggested: (IPython, RRID:SCR_001658)
    Boxplots for tissues of relevance were generated using Matplotlib and Seaborn libraries.
    Matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)
    ] Python library to identify possible enriched terms in biological process (BP), molecular function (MF), cellular component (CC), human phenotype (HP), KEGG pathway, and WikiPathways (WP) ontologies.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    WikiPathways
    suggested: (WikiPathways, RRID:SCR_002134)
    ACE2 protein expression: Immunohistochemical localization of human ACE2 was evaluated from immunostained specimens provided by Protein Expression Atlas (https://www.proteinatlas.org/).
    https://www.proteinatlas.org/
    suggested: (HPA, RRID:SCR_006710)
    According to Protein Expression Atlas the immunostainings were performed with the rabbit anti-human polyclonal antibody (HPA000288; Sigma Aldrich, St. Louis, MO) raised against 111 N-terminal amino acids of ACE2 and diluted 1:250 for the staining.
    HPA000288; Sigma Aldrich
    suggested: None
    Promoter Analysis: Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https://github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: ATAC-Seq data from ENCODE [64]
    ENCODE
    suggested: (Encode, RRID:SCR_015482)
    , transcription start sites and expression data from FANTOM5 [65], expression quantitative trail loci from GTEx [66], TFBS metacluster data from GTRD [67], TFBS binding profile data from JASPAR [68], and sequence and conservation data from Ensembl [69].
    JASPAR
    suggested: (JASPAR, RRID:SCR_003030)
    Ensembl
    suggested: (Ensembl, RRID:SCR_002344)
    Batch correction by individual and sample region was performed with SCANPY using the ComBat function.
    ComBat
    suggested: (ComBat, RRID:SCR_010974)
    Comparisons of ACE2 expression values in different tissues and between groups delineated by age or sex, were carried out by one-way ANOVA using the stats package in the SciPy [62
    SciPy
    suggested: (SciPy, RRID:SCR_008058)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    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.

  3. Version published to 10.1101/2020.04.13.038752 on bioRxiv