Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells

Article activity feed

1. 

   ScreenIT

   Sep 21, 2020

   SciScore for 10.1101/2020.09.18.302398: (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

   Antibodies
   Sentences	Resources
   Cells were then washed with PBS, fixed in 4% paraformaldehyde (PFA) in PBS for 15 minutes, washed again with PBS, permeabilized with 0.2% saponin in blocking buffer (2% BSA, 2% FBS in PBS) for 30 minutes at room temperature (RT), and incubated with 1:1000 mouse antibody specific for SARS-CoV-2 nucleocapsid protein (Sino Biological, Beijing, China 40143-MM05) overnight at 4°C in blocking buffer consisting of 2% FBS and 2% BSA.	SARS-CoV-2 nucleocapsid protein

   SciScore for 10.1101/2020.09.18.302398: (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

   Antibodies
   Sentences	Resources
   Cells were then washed with PBS, fixed in 4% paraformaldehyde (PFA) in PBS for 15 minutes, washed again with PBS, permeabilized with 0.2% saponin in blocking buffer (2% BSA, 2% FBS in PBS) for 30 minutes at room temperature (RT), and incubated with 1:1000 mouse antibody specific for SARS-CoV-2 nucleocapsid protein (Sino Biological, Beijing, China 40143-MM05) overnight at 4°C in blocking buffer consisting of 2% FBS and 2% BSA.	SARS-CoV-2 nucleocapsid protein suggested: (Bioss Cat# bsm-41414M, RRID:AB_2848129)
   The following day, plates were washed 3X with PBS, incubated with a 1:1000 dilution of goat anti-mouse AlexaFluor647 antibody (Abcam, Cambridge, United Kingdom) and DAPI/Hoechst (Invitrogen) in blocking buffer for 1h at RT, washed again 3x with PBS, fixed in 4% PFA, and replaced in PBS.	anti-mouse suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells and virus: Vero E6 and Calu-3 cells (Calu-3:ATCC HTB-55; Vero E6: ATCC, CRL-1586) were maintained in high glucose DMEM (Gibco, Waltham, MA, USA) supplemented with 10% FBS (R&D Systems, Minneapolis, MN, USA), 1X GlutaMAX (Gibco, Waltham, MA, USA), and 1X PenStrep (Gibco, Waltham, MA, USA) at 37°C and 5% CO2.	Vero E6 suggested: None
   2500 Vero E6 (12 μl/well) or 10000 Calu-3 (12μl/well) were seeded in 384-well white optical-bottom tissue culture plates (Nunc) with the Multidrop Combi liquid handling instrument (Thermo Fisher Scientific, Waltham, MA).	Calu-3 suggested: None
   Software and Algorithms
   Sentences	Resources
   The data was plotted and analyzed with spotfire (Tibco) and GraphPad Prism.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   GSEA Analysis: Compounds were annotated with targets, pathways and mechanisms of actions using the Center for Emerging and Neglected Diseases’ database and for pharmacokinetic data and transporter inhibition data, the DrugBank database 42.	GSEA suggested: (SeqGSEA, RRID:SCR_005724) DrugBank suggested: (DrugBank, RRID:SCR_002700)
   Images were analyzed for N stain per nuclei with the CellProfiler 3.1.9 software (Broad Institute, Cambridge, MA).	CellProfiler suggested: None
   Custom code written in MATLAB (available at https://gitlab.com/tjian-darzacq-lab/second-derivative-cq-analysis) was used to take the numerical second derivative of fluorescence intensity with respect to cycle number, using a sliding window of ± 3 cycles.	MATLAB suggested: (MATLAB, RRID:SCR_001622)

   ---

   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 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.

   ---

   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.

   ---

   Read the original source
2. 

   Version published to 10.1101/2020.09.18.302398 on bioRxiv

   Sep 18, 2020