1. SciScore for 10.1101/2021.04.12.438219: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: These studies were approved by the competent local human ethics committee (ID:2017-00734).
    RandomizationThe genotypes of the mice could not be blinded or randomized, due to the experimental design.
    BlindingThe genotypes of the mice could not be blinded or randomized, due to the experimental design.
    Power Analysisnot detected.
    Sex as a biological variableTo exclude non-haematopoietic deletion, total bone marrow (BM) was isolated from wildtype (Rnh1fl/fl) or Rnh1fl/fl Mx1-Cre+ mice and transplanted (7×106 BM cells) into lethally irradiated CD45.1+ congenic recipient mice (8 weeks old male mice) (B6.SJL-PtprcaPepcb/BoyCrl, from Charles river).
    Cell Line AuthenticationContamination: All the generated THP1 and iMAC clones were tested negative for mycoplasma contamination using MycoAlert Mycoplasma Detection Kit (Lonza, Cat#LT07-318).

    Table 2: Resources

    Antibodies
    SentencesResources
    Biopsies were stained with human RNH1 antibody from Prestige Antibodies® Sigma (HPA039223).
    HPA039223
    suggested: None
    Anti-human IL-1β antibody (12242), anti-NFκB2 (p100), anti-IκBα, anti-Phospho-IκBα, anti-GFP (2555) from Cell signalling.
    Anti-human IL-1β
    suggested: None
    anti-NFκB2
    suggested: None
    anti-IκBα
    suggested: (Active Motif Cat# 40904, RRID:AB_2793427)
    anti-Phospho-IκBα
    suggested: None
    anti-GFP
    suggested: (Cell Signaling Technology Cat# 2555, RRID:AB_10692764)
    Anti-mouse IL-1β antibody (AF-401-NA) from R&D.
    Anti-mouse IL-1β
    suggested: (R and D Systems Cat# AF-401-NA, RRID:AB_416684)
    Anti-β-Actin from Abcam.
    Anti-β-Actin
    suggested: None
    Using these whole cell lysates, immuno-precipitation was performed with Ubiquitin antibody (Sc-8017, Santa Cruz Biotechnology) bound to Dynabeads Protein G (10003D, Life Technologies) for 3 hours with rotation at 4°C.
    Ubiquitin
    suggested: None
    Sc-8017
    suggested: (Santa Cruz Biotechnology Cat# sc-8017 AC, RRID:AB_2762364)
    After blocking, cells were incubated overnight at 4 °C with the primary antibodies against ASC (HASC-71, BioLegend).
    ASC
    suggested: (BioLegend Cat# 653904, RRID:AB_2564508)
    HASC-71
    suggested: None
    Anti-RNH1 (Prestige Antibodies® Sigma, HPA039223) was added overnight at 1:500, followed by anti-rabbit secondary, ABC amplification and DAB detection (both ThermoFisher).
    Anti-RNH1
    suggested: (Sigma-Aldrich Cat# HPA039223, RRID:AB_10795581)
    anti-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cells and cell culture media: Mouse bone marrow derived macrophages (BMDM), iMACs (immortalized macrophages) and Human THP-1 cells were used for inflammasome activation experiments.THP-1 cells and iMACs were grown in RPMI 1640 GlutaMAX™-I medium (Invitrogen) were supplemented with 10% (vol/vol) FBS (Amimed), 1% of penicillin and streptomycin (PAA Laboratories), at 37 °C and 5% CO2.
    THP-1
    suggested: None
    THP1 cells were obtained from ATCC and iMAC cells were provided by Petr Broz (University of Lausanne).
    THP1
    suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
    Retroviral vector pMSCVpuro-Flag–RNH1 was co-transfected with the helper plasmids VSV-G and Hit60 into HEK293T cells using PEI transfection reagent.
    HEK293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Experimental Models: Organisms/Strains
    SentencesResources
    Details of Rnh1 conditional-knockout mice generation and mouse experiments: Rnh1 conditional-knockout (Rnh1fl/fl) mice were generated on a C57BL/6 background.
    Rnh1fl/fl
    suggested: None
    C57BL/6
    suggested: None
    5A) was electroporated into (C57BL/6) embryonic stem (ES) cells. Targeted (C57BL/6 FLP) embryonic stem cells were microinjected into Balb/c blastocysts.
    C57BL/6 FLP
    suggested: None
    Resulting chimeras with a high percentage black coat colour were mated to C57BL/6 WT mice to generate Neo deleted, F1 heterozygous offspring.
    C57BL/6 WT
    suggested: None
    We crossed Rnh1fl/fl mice with Mx1-Cre mouse strain (Jackson: 002527) to generate inducible mouse model (Rnh1fl/fl Mx1-Cre+).
    Mx1-Cre
    suggested: None
    Rnh1fl/fl Mx1-Cre+
    suggested: None
    To exclude non-haematopoietic deletion, total bone marrow (BM) was isolated from wildtype (Rnh1fl/fl) or Rnh1fl/fl Mx1-Cre+ mice and transplanted (7×106 BM cells) into lethally irradiated CD45.1+ congenic recipient mice (8 weeks old male mice) (B6.SJL-PtprcaPepcb/BoyCrl, from Charles river).
    B6.SJL-PtprcaPepcb/BoyCrl
    suggested: RRID:IMSR_CRL:494)
    Software and Algorithms
    SentencesResources
    Data were analysed by using FlowJo (version 9.3.1, TreeStar Inc) software.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Images were captured with inverted confocal microscope LSM 710 (Zeiss) and analyzed with ImageJ across at least 10 fields from three independent experiments.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    Images were analysed using Zen Lite software (Zeiss).
    Zen Lite
    suggested: None
    From Blast output, selected protein sequences (excluding the isoforms and model refseq proteins) were aligned using MAFFT multiple sequence aligner (Katoh and Standley, 2013).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Sequence conservation analysis was performed on IQ-Tree webserver (http://iqtree.cibiv.univie.ac.at/) using ultrafast bootstrap analysis with 1,000 number of bootstrap alignments (Katoh and Standley, 2013) Circular tree was visualized using Interactive Tree Of Life (iTOL) (Letunic and Bork, 2019).
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)
    All statistical analyses were calculated using Graph Pad Prism version 8.
    Graph Pad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04510012RecruitingCharacterizing the Immune Response and Neuronal Damage in CO…


    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.

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