Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses

  1. Ruona Shi
  2. Zhenhuan Feng
  3. Xiaofei Zhang

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Abstract

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  1. Version published to 10.1016/j.gpb.2021.09.007
  2. ScreenIT

    SciScore for 10.1101/2021.07.19.452910: (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
    or with 1 μg UBE2O antibody (A301-873A, Bethyl) overnight following with 15 μL prewashed protein A/G beads (1:1 mixture, 1614013 and 1614023, Biorad) incubation for another 1.5 hr.
    UBE2O
    suggested: (Thermo Fisher Scientific Cat# A301-873A, RRID:AB_1309799)
    Antibodies used in these experiments included Flag (F1804, Sigma), EGFP (50430-2-AP, Proteintech), NSP3 (ab181602, Abcam), UBE2O (A301-873A, Bethyl), pSerine (gtx26639, GeneTex), pThreonine (9386, Cell Signaling), TAB2 (A302-759A, Bethyl), TAB3 (A302-208A, Bethyl)
    EGFP
    suggested: None
    A301-873A , Bethyl) , pSerine ( gtx26639 , GeneTex) , pThreonine ( 9386 , Cell Signaling) , TAB2
    suggested: None
    A302-759A , Bethyl) , TAB3
    suggested: None
    Antibodies used for the experiment are: CANX (2679, Cell Signaling), TOMM20 (ab56783, Abcam), Flag (F1804 and F7425, Sigma), NSP3 (ab181602, Abcam).
    CANX ( 2679 , Cell Signaling)
    suggested: (Cell Signaling Technology Cat# 2679, RRID:AB_2228381)
    TOMM20
    suggested: (Abcam Cat# ab56783, RRID:AB_945896)
    ab56783 , Abcam) , Flag ( F1804
    suggested: None
    NSP3
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    HEK293T cells from ATCC were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone, SH30033.01) supplemented with 10% Fetal bovine serum (FBS, Hyclone, SV30160.03) and 1×Penicillin/Streptomycin (Hyclone,
    HEK293T
    suggested: None
    Recombinant DNA
    SentencesResources
    UBE2O plasmid was described before [52] and TNIP cDNA was amplified from HeLa cDNA and cloned in to pCS2 vector with Flag tag.
    pCS2
    suggested: RRID:Addgene_62214)
    Software and Algorithms
    SentencesResources
    Raw data were first transformed using FAIMS MzXML Generator and then analyzed using MaxQuant version 1.6.17.0 [54]
    MaxQuant
    suggested: (MaxQuant, RRID:SCR_014485)
    Protein-Protein Interaction (PPI) network and pathway annotation of interactors was constructed by Cytoscape plugin Reactome FI v7.2.3 [57].
    Cytoscape
    suggested: (Cytoscape, RRID:SCR_003032)
    Interactors of NSP3 were divided into 3 groups (CoV1, CoV2 and both) and enriched GO terms were shown using clusterProfiler package [58]
    clusterProfiler
    suggested: (clusterProfiler, RRID:SCR_016884)
    Circos plots was performed using circlize package [59].
    Circos
    suggested: (Circos, RRID:SCR_011798)
    circlize
    suggested: (circlize, RRID:SCR_002141)
    We filtered out the kinases of which matching sites was less than 3 or Z-score is lower than 1 and created Human Kinome Tree illustration using KinMap [36].
    KinMap
    suggested: None
    The targeting drugs that regulate activity changed kinases were extracted from drugbank (https://go.drugbank.com/).
    drugbank
    suggested: (DrugBank, RRID:SCR_002700)
    Transcriptome data analysis: Raw reads were aligned to the human genome (hg38) using HISAT2 [62].
    HISAT2
    suggested: (HISAT2, RRID:SCR_015530)
    Next, we assembled reads to transcripts and quantified the read counts of each genes utilizing StringTie [63].
    StringTie
    suggested: (StringTie , RRID:SCR_016323)
    We kept genes that CPM is greater than 1 in at least 2 samples and analyzed the differential expression gene using edgeR [64].
    edgeR
    suggested: (edgeR, RRID:SCR_012802)
    , Molecular Function (MF) were performed using enrichR in clusterProfiler package.
    enrichR
    suggested: (Enrichr, RRID:SCR_001575)

    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.

  3. Version published to 10.1101/2021.07.19.452910v1 on bioRxiv