Generation of glucocorticoid-resistant SARS-CoV-2 T cells for adoptive cell therapy

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1. Version published to 10.1016/j.celrep.2021.109432

   Jul 1, 2021
2. 

   ScreenIT

   Sep 21, 2020

   SciScore for 10.1101/2020.09.15.298547: (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.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cells were subsequently stained with antibodies against IL-2 PE (BD Biosciences, Clone MQ1-17H12), IFN-γ BV450 (BD Biosciences, Clone B27), and TNF-α AF700 (Biolegend	IL-2 PE suggested: None TNF-α suggested: None
   SARS-CoV-2 antibody assay: IgM and IgG responses against nucleocapsid, S1 receptor-binding domain (RBD), S1S2, S2, S1, OC43, HKU1, NL63 Nucleoprotein, and 229E Spike derived from SARS-CoV-2 and other human coronaviruses were performed at Genalyte (Austin, TX) CLIA-certified laboratory …

   SciScore for 10.1101/2020.09.15.298547: (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.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cells were subsequently stained with antibodies against IL-2 PE (BD Biosciences, Clone MQ1-17H12), IFN-γ BV450 (BD Biosciences, Clone B27), and TNF-α AF700 (Biolegend	IL-2 PE suggested: None TNF-α suggested: None
   SARS-CoV-2 antibody assay: IgM and IgG responses against nucleocapsid, S1 receptor-binding domain (RBD), S1S2, S2, S1, OC43, HKU1, NL63 Nucleoprotein, and 229E Spike derived from SARS-CoV-2 and other human coronaviruses were performed at Genalyte (Austin, TX) CLIA-certified laboratory using plasma from convalescent patients.	HKU1 , NL63 Nucleoprotein , suggested: None
   Cells were washed twice with perm/wash buffer, stained with antibodies directed against intracellular markers and after an additional wash step, stored overnight in 500 µl of 1.6% paraformaldehyde (EMD Biosciences)/PBS with 125 nM iridium nucleic acid intercalator (Fluidigm).	iridium nucleic acid intercalator ( Fluidigm) . suggested: None
   ) XP rabbit monoclonal antibody and β-actin antibody (clone 8H10D10); both antibodies were obtained from Cell Signaling Technology.	β-actin suggested: (Cell Signaling Technology Cat# 3700, RRID:AB_2242334)
   Software and Algorithms
   Sentences	Resources
   Data analysis was performed using Flowjo (Tree Star, Ashland, OR).	Flowjo suggested: (FlowJo, RRID:SCR_008520)
   Data dimensionality reduction was performed using the R package Rtsne (v0.15) for t-Distributed Neighbor Embedding (tSNE) analysis.	Rtsne suggested: (Rtsne, RRID:SCR_016342)
   The R package Rphenograph (v0.99.1) was used to cluster all cells into 32 clusters.	Rphenograph suggested: None
   The t-SNE plots were generated using the R package ggplot2 (v3.3.2).	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Normalized mean values of marker expressions in each cluster were plotted as heatmap using the function “pheatmap” from R package pheatmap (v1.0.12).	pheatmap suggested: (pheatmap, RRID:SCR_016418)
   Gel images were obtained using GeneSys software in a G:BOX gel documentation system (Syngene).	GeneSys suggested: (GeneSys, RRID:SCR_015770)

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   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).

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04315948	Active, not recruiting	Trial of Treatments for COVID-19 in Hospitalized Adults

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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 10.1101/2020.09.15.298547 on bioRxiv

   Sep 15, 2020