Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms
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SciScore for 10.1101/2020.07.10.197079: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell Culture and SARS-CoV-2 Infection: VeroE6 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS). VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Software and Algorithms Sentences Resources All structures output from the SuperFold prediction were visualized and drawn using StructureEditor, a tool in the RNAStructure software suite(Reuter and Mathews, 2010). RNAStructuresugge…SciScore for 10.1101/2020.07.10.197079: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Cell Culture and SARS-CoV-2 Infection: VeroE6 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS). VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Software and Algorithms Sentences Resources All structures output from the SuperFold prediction were visualized and drawn using StructureEditor, a tool in the RNAStructure software suite(Reuter and Mathews, 2010). RNAStructuresuggested: (RNAstructure, RRID:SCR_017216)All sequences referenced below were downloaded from the NCBI Taxonomy browser(Benson et al., 2018). Taxonomysuggested: (Taxonomy, RRID:SCR_004299)Synonymous mutation rate analysis: All codon alignments were visualized and edited using Jalview v 2.11.0(Waterhouse et al., 2009). Jalviewsuggested: (Jalview, RRID:SCR_006459)Results from OddPub: Thank you for sharing your code and data.
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.
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