SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators

  1. İlkay Çisil Köksaldı
  2. Sıla Köse
  3. Recep Erdem Ahan
  4. Nedim Hacıosmanoğlu
  5. Ebru Şahin Kehribar
  6. Murat Alp Güngen
  7. Aliye Baştuğ
  8. Bedia Dinç
  9. Hürrem Bodur
  10. Aykut Özkul
  11. Urartu Özgür Şafak Şeker

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Abstract

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  1. Version published to 10.1021/acs.analchem.1c00886
  2. ScreenIT

    SciScore for 10.1101/2020.07.28.20164004: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Overall, 503 trigger candidates designed with Primer-BLAST, 123 candidates have passed the minimum energy and BLAST requirements, and 5 trigger candidates resulted in up to 4 different switch constructs.
    Primer-BLAST
    suggested: (Primer-BLAST, RRID:SCR_003095)
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)

    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.

  3. ScreenIT

    SciScore for 10.1101/2020.07.28.20164004: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Toehold triggers are then generated using NCBI Primer BLAST.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Eligible candidates were then used in the design of their respective toehold switches in silico using NUPACK© software. c) Validation of designed toehold switches.
    NUPACK©
    suggested: None
    For the generation of trigger sequence candidates with primer sites, we used Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) by using temperature parameters adjusted to 60ºC and PCR product size between 120-160 bp.
    Primer-BLAST
    suggested: (Primer-BLAST, RRID:SCR_003095)

    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 Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. ScreenIT

    SciScore for 10.1101/2020.07.28.20164004: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Selected sequences are aligned using BLAST against the genomes of human and closely related viruses to SARS-CoV-2 to exclusively select SARS-CoV-2 specific triggers.
    BLAST
    suggested: (BLASTX, SCR_001653)
    Eligible candidates were then used in the design of their respective toehold switches in silico using NUPACK© software. c) Validation of designed toehold switches.
    NUPACK©
    suggested: None
    Overall, 503 trigger candidates designed with Primer-BLAST, 123 candidates have passed the minimum energy and BLAST requirements, and 5 trigger candidates resulted in up to 4 different switch constructs.
    Primer-BLAST
    suggested: (Primer-BLAST, SCR_003095)

    Data from additional tools added to each annotation on a weekly basis.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  5. Version published to 10.1101/2020.07.28.20164004v1 on medRxiv