ILRUN Downregulates ACE2 Expression and Blocks Infection of Human Cells by SARS-CoV-2

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1. Version published to 10.1128/jvi.00327-21

   Jul 12, 2021
2. 

   ScreenIT

   Nov 17, 2020

   SciScore for 10.1101/2020.11.13.381343: (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 subsequently stained with 1/1,000 dilution of an anti-rabbit AF488 antibody (Invitrogen catalogue number A11008).	anti-rabbit suggested: (Molecular Probes Cat# A-11008, RRID:AB_143165)
   Experimental Models: Cell Lines
   Sentences	Resources
   Caco-2 cells were maintained in Gibco Modified Eagles Medium (MEM) supplemented with 20 % (v/v) FCS, 10 mM HEPES, 0.1 mM non-essential amino acids, 2 mM glutamine, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 …

   SciScore for 10.1101/2020.11.13.381343: (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 subsequently stained with 1/1,000 dilution of an anti-rabbit AF488 antibody (Invitrogen catalogue number A11008).	anti-rabbit suggested: (Molecular Probes Cat# A-11008, RRID:AB_143165)
   Experimental Models: Cell Lines
   Sentences	Resources
   Caco-2 cells were maintained in Gibco Modified Eagles Medium (MEM) supplemented with 20 % (v/v) FCS, 10 mM HEPES, 0.1 mM non-essential amino acids, 2 mM glutamine, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin (Life Technologies).	Caco-2 suggested: None
   The isolate of SARS-CoV-2 (BetaCoV/Australia/VIC01/2020) was received from the Victorian Infectious Disease Reference Laboratory (VIDRL, Melbourne, Australia) and passaged in VeroE6 cells for isolation, followed by passaging in VeroE6 cells for stock generation.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Software and Algorithms
   Sentences	Resources
   http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ suggested: (FastQC, RRID:SCR_014583)
   Bioinformatic analysis of RNA-seq data: Quality and adapter trimming was performed using TrimGalore v0.6.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default settings for automatic adapter detection.	TrimGalore suggested: None http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ suggested: (Trim Galore, RRID:SCR_011847)
   Trimmed reads were mapped to the National Cener for Biotechnology Information (NCBI) human reference genome (GRCh38) downloaded from Illumina iGenomes (http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/NCBI/GRCh38/Homo_sapiens_NCBI_GRCh38.ta r.gz) using Tophat v2.1.1 (49).	Tophat suggested: (TopHat, RRID:SCR_013035)
   The number of reads overlapping each gene in the NCBI annotated reference genome (GRCh38) were counted using htseq-count v0.11.2 within Python v3.7.2 (50), using the intersection-nonempty mode to handle reads overlapping more than one feature.	htseq-count suggested: (htseq-count, RRID:SCR_011867)
   The Bioconductor package DESeq2 was used to test for differential expression between different experimental groups (51).	Bioconductor suggested: (Bioconductor, RRID:SCR_006442) DESeq2 suggested: (DESeq, RRID:SCR_000154)
   KEGG) pathway mapping (52), custom python scripts were used to prepare input lists for conversion of gene symbols to Entrez gene IDs using bioDBnet’s db2db tool (https://biodbnet-abcc.ncifcrf.gov/db/db2db.php) and generation of hex codes based on fold change for colour mapping of KEGG pathways (https://www.genome.jp/kegg/tool/map_pathway2.html).	KEGG suggested: (KEGG, RRID:SCR_012773) python suggested: (IPython, RRID:SCR_001658)
   Trimmed reads were mapped to a SARS-CoV-2 reference genome of the virus used in experiments (MT007544; SARS-CoV-2/human/AUS/VIC01/2020) using bowtie v2.3.4 (53).	bowtie suggested: (Bowtie, RRID:SCR_005476)
   Mapped viral reads were counted using samtools v1.10.0 (Li et al., 2009) and coverview v1.4.4 (54) then normalised to library read content.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Analysis of publicly available data: The NCBI Gene Expression Omnibus was searched for suitable RNA-seq datasets and GSE Accession number entered into the GREIN : GEO RNA-seq Experiments Interactive Navigator (http://www.ilincs.org/apps/grein/) to retrieve metadata and normalized counts.	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   Normalised counts were plotted for each gene using ggplot2 package in R.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Statistics: The difference between two groups was analysed in GraphPad Prism by a two-tailed Student’s t test and between multiple groups by one-way ANOVA.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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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: 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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3. 

   Version published to 10.1101/2020.11.13.381343v1 on bioRxiv

   Nov 13, 2020