The SARS-CoV-2 Nsp3 macrodomain reverses PARP9/DTX3L-dependent ADP-ribosylation induced by interferon signaling

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1. Version published to 10.1016/j.jbc.2021.101041

   Sep 1, 2021
2. 

   ScreenIT

   Apr 9, 2021

   SciScore for 10.1101/2021.04.06.438552: (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	Authentication: For most experiments, 6×6 adjacent fields of view were acquired per sample using automated autofocus and image acquisition settings.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Primers and Antibodies: All oligonucleotides and antibodies used in this study are presented in the tables below:	Antibodies suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK293 FT cells were grown in DMEM/high glucose supplemented with 10% FBS (Thermo), 50mg/mL gentamycin (Sigma), 1mM sodium pyruvate …

   SciScore for 10.1101/2021.04.06.438552: (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	Authentication: For most experiments, 6×6 adjacent fields of view were acquired per sample using automated autofocus and image acquisition settings.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Primers and Antibodies: All oligonucleotides and antibodies used in this study are presented in the tables below:	Antibodies suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK293 FT cells were grown in DMEM/high glucose supplemented with 10% FBS (Thermo), 50mg/mL gentamycin (Sigma), 1mM sodium pyruvate (Thermo), non essential amino acids (Thermo) and 2mM L-glutamine (Thermo).	HEK293 suggested: None
   These vectors were co-transfected with psPAX2 and pMD2.G packaging vectors (Systems Biosciences) into HEK-293FT cells using standard PEI transfection, the supernatant collected 48h and 72h after transfection, filtered through 0.45 μm filters and used to transduce A549 cells in the presence of 8 μg/mL polybrene (Sigma).	HEK-293FT suggested: ATCC Cat# PTA-5077, RRID:CVCL_6911) A549 suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
   Software and Algorithms
   Sentences	Resources
   HEK293 FT cells were grown in DMEM/high glucose supplemented with 10% FBS (Thermo), 50mg/mL gentamycin (Sigma), 1mM sodium pyruvate (Thermo), non essential amino acids (Thermo) and 2mM L-glutamine (Thermo).	Thermo suggested: (Thermo Xcalibur, RRID:SCR_014593)
   Molecular docking simulations were performed with Gold 5.4 and AutoDock 4.2.3 softwares.	AutoDock suggested: (AutoDock, RRID:SCR_012746)
   Signals were quantified using ImageJ software.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   This cDNA was used for qPCR (5 ng/reaction) using Power SYBR green Master mix (Thermo) with three technical replicates per biological replicate, using 200 nM of the primer sets indicated in Table 1, which were chosen from PrimerBank (Wang et al, 2012).	PrimerBank suggested: (PrimerBank, RRID:SCR_006898)
   All graphs and statistical analyses were generated using GraphPad Prism software and display mean ± SEM of the normalized values relative to the IFNγ-treated control for each replicate, considered as 100%.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your 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: Please consider improving the rainbow (“jet”) colormap(s) used on page 26. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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3. 

   Version published to 10.1101/2021.04.06.438552v1 on bioRxiv

   Apr 7, 2021