Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

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1. Version published to 10.1016/j.celrep.2021.109108

   May 1, 2021
2. 

   ScreenIT

   Dec 27, 2020

   SciScore for 10.1101/2020.12.22.423893: (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	Contamination: The cell lines were tested for presence of mycoplasma using the MycoAlert Mycoplasma Detection Kit (Lonza)

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   , Caco-2 (human intestinal epithelial cells, ATCC HTB-37) and Calu-3 (human lung epithelial cells, ATCC HTB-55) and maintained at 37 °C, 5% (v/v) CO2.	Caco-2 suggested: None
   Oxford Nanopore Technologies library preparation and sequencing: Direct cDNA sequencing libraries were prepared using an input of 3 μg of total RNA (equivalent …

   SciScore for 10.1101/2020.12.22.423893: (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	Contamination: The cell lines were tested for presence of mycoplasma using the MycoAlert Mycoplasma Detection Kit (Lonza)

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   , Caco-2 (human intestinal epithelial cells, ATCC HTB-37) and Calu-3 (human lung epithelial cells, ATCC HTB-55) and maintained at 37 °C, 5% (v/v) CO2.	Caco-2 suggested: None
   Oxford Nanopore Technologies library preparation and sequencing: Direct cDNA sequencing libraries were prepared using an input of 3 μg of total RNA (equivalent to approximately 150 ng of poly(A) + RNA) for Vero cell infections, and 1-2 μg of total RNA (equivalent to approximately 50 – 100 ng of poly(A) + RNA) for Caco-2 and Calu-3 cell infections per triplicate.	Calu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   + RNA) for Vero cell infections and 3 μg of total RNA (1 μg per triplicate equivalent to ∼150 ng poly(A)	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   All libraries were sequenced with MinION R9.4.1 flow cells.	MinION suggested: (MinION, RRID:SCR_017985)

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   Results from OddPub: Thank you for sharing your code and data.

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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

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   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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   Read the original source
3. 

   Version published to 10.1101/2020.12.22.423893v1 on bioRxiv

   Dec 22, 2020