Oral Hsp90 inhibitor SNX-5422 attenuates SARS-CoV-2 replication and dampens inflammation in airway cells

Article activity feed

1. Version published to 10.1016/j.isci.2021.103412

   Dec 1, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.23.432479: (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
   The cells were then incubated with anti-SARS-CoV-2 N protein antibody (Sinobiological; 1:100) for 2hrs at room temperature.	anti-SARS-CoV-2 N protein suggested: None
   After subsequent washing of the samples, the cells were treated with Alexa Fluor 488 donkey anti-rabbit secondary antibody (Invitrogen; 1:1000) for 1hr at room temperature.	anti-rabbit suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Calu-3 cells (ATCC) were cultured in Dulbecco’s …

   SciScore for 10.1101/2021.02.23.432479: (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
   The cells were then incubated with anti-SARS-CoV-2 N protein antibody (Sinobiological; 1:100) for 2hrs at room temperature.	anti-SARS-CoV-2 N protein suggested: None
   After subsequent washing of the samples, the cells were treated with Alexa Fluor 488 donkey anti-rabbit secondary antibody (Invitrogen; 1:1000) for 1hr at room temperature.	anti-rabbit suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Calu-3 cells (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum (FBS), 25mM HEPES, 1X Penicillin/Streptomycin (Gibco), and maintained at 37°C in 5% CO2.	Calu-3 suggested: None
   Briefly, 0.72 × 106 Vero E6 cells were seeded in 6 well plates.	Vero E6 suggested: RRID:CVCL_XD71)
   Software and Algorithms
   Sentences	Resources
   The stained cells were fixed using methanol-free 4% formaldehyde (Thermo Fisher) for 30 minutes and acquired on an LSRII flow cytometer (BD Biosciences) using BD FACS Diva software and analyzed with FlowJo software version 10.1	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Images were captured with 20X objective, processed using Zeiss Zen Black software and proportion of SARS-CoV-2-infected cells were counted using Fiji, utilizing the analyze particle function.	Zeiss Zen Black suggested: (Black Zen software, RRID:SCR_018163) Fiji suggested: (Fiji, RRID:SCR_002285)
   CC50 and IC50 calculations: CC50 and IC50 were calculated using Graph Pad Prism using curve fitting.	Graph Pad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Analysis of the bulk RNA-seq data: RNA-Seq data was quality checked with FastQC (Andrews, 2010) and preprocessing was carried out using TrimGalore (Krueger) toolkit to trim low-quality bases and Illumina adapter sequences using default settings.	FastQC suggested: (FastQC, RRID:SCR_014583)
   Reads were aligned to the ENSEMBL Homo_sapiens.GRCh38.dna.primary_assembly genome using the ENSEMBL Homo_sapiens.GRCh38.100 transcript (Kersey et al., 2012) annotation file with STAR (Dobin et al., 2013)	ENSEMBL suggested: (Ensembl, RRID:SCR_002344) STAR suggested: (STAR, RRID:SCR_015899)
   Gene level counts were quantified using FeatureCounts (Liao et al., 2014) tool, counting unique features in non-stranded mode and retaining both gene ID, gene name, and gene biotype mapping from the ENSEMBL annotation file.	FeatureCounts suggested: (featureCounts, RRID:SCR_012919)
   Normalization and differential expression were carried out with DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package, utilizing the ‘apeglm’ Bioconductor package (Zhu et al., 2019) for log fold change shrinkage, in R statistical programming environment.	DESeq2 suggested: (DESeq, RRID:SCR_000154) Bioconductor suggested: (Bioconductor, RRID:SCR_006442)
   Dot plots demonstrating upregulated and downregulated KEGG pathways were generated using ‘ClusterProfiler’ package in R using a “universe” of all human genes.	KEGG suggested: (KEGG, RRID:SCR_012773)
   Protein-protein interaction (PPI) network was constructed using STRING and Cytoscape (vs 3.8.2).	STRING suggested: (STRING, RRID:SCR_005223) Cytoscape suggested: (Cytoscape, RRID:SCR_003032)
   Data and code availability: The raw and processed RNA-seq data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE166397 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE166397).	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)

   ---

   Results from OddPub: Thank you for sharing your 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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.02.23.432479v1 on bioRxiv

   Feb 23, 2021