The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

  1. Omer Ziv
  2. Jonathan Price
  3. Lyudmila Shalamova
  4. Tsveta Kamenova
  5. Ian Goodfellow
  6. Friedemann Weber
  7. Eric A. Miska

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Abstract

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  1. Version published to 10.1016/j.molcel.2020.11.004
  2. Version published to 10.1101/2020.07.19.211110v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.07.19.211110: (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
    Cell lines: Chlorocebus sabaeus (Green monkey) VeroE6 (female, RRID:CVCL_YQ49) were purchased from American Type Culture Collection (ATCC, id: ATCC CRL-1586).
    detected: (JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    VeroE6/TMPRSS2 cells (female, doi: 10.1073/pnas.2002589117) were kindly provided by Prof. Dr. Stefan Pöhlmann (German Primate Center,
    VeroE6/TMPRSS2
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    HuH7 (Homo sapiens, male, adult hepatocellular carcinoma, RRID:CVCL_0336) cells were purchased from the Japanese Collection of Research Bioresources (JCRB) Cell Bank (JCRB No. JCRB0403) and cultured in Dulbecco’s modified Eagles medium (DMEM) supplemented with 10% fetal bovine serum at 37 °C in a humidified CO2 incubator.
    HuH7
    detected: (KCB Cat# KCB 200970YJ, RRID:CVCL_0336)
    Titration of virus stocks was conducted using Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    For MERS infection, HuH7 cells were inoculated with MERS-CoV strain EMC/2012 (GenBank: JX869059.2; PMID: 23170002) at MOI=2 pfu/cell for 20 hours.
    HuH7
    suggested: None
    Software and Algorithms
    SentencesResources
    To identify densely connected subgraphs (communities) with chimeric groups containing chimeric reads that originated from the same structure, we clustered the graph using random walks with the cluster_waltrap function (steps = 2) from the iGraph package.
    iGraph
    suggested: (igraph, RRID:SCR_019225)
    Sequence conservation analysis of the extended FSE structure: Genome conservation data analyzed with synplot2 (Firth, 2014) was taken from (Firth, 2020).
    Genome
    suggested: (JGI Genome Portal, RRID:SCR_002383)

    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.

    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.

  4. Version published to 10.1101/2020.07.19.211110v1 on bioRxiv