Epigenetic Regulator miRNA Pattern Differences Among SARS-CoV, SARS-CoV-2, and SARS-CoV-2 World-Wide Isolates Delineated the Mystery Behind the Epic Pathogenicity and Distinct Clinical Characteristics of Pandemic COVID-19

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1. Version published to 10.3389/fgene.2020.00765

   Jul 10, 2020
2. 

   ScreenIT

   Jun 7, 2020

   SciScore for 10.1101/2020.05.06.081026: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   2.8 RNA-seq expression data analysis: RNA-seq raw read-count data on SARS-CoV-2 mediated expression changes in primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells were obtained from the GEO database (GSE147507) (Barrett et al., 2012).	A549 suggested: None
   Software and Algorithms
   Sentences	Resources
   2.1 Obtaining SARS-CoV and SARS-CoV2 Genome sequences: The reference genome of SARS-CoV (RefSeq Accession no. NC_004718.3) and SARS-CoV-2 (RefSeq Accession no. NC_045512.2) was fetched from NCBI RefSeq database (NCBI-RefSeq, 2020).	RefSeq suggested: (RefSeq, RRID:SCR_…

   SciScore for 10.1101/2020.05.06.081026: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   2.8 RNA-seq expression data analysis: RNA-seq raw read-count data on SARS-CoV-2 mediated expression changes in primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells were obtained from the GEO database (GSE147507) (Barrett et al., 2012).	A549 suggested: None
   Software and Algorithms
   Sentences	Resources
   2.1 Obtaining SARS-CoV and SARS-CoV2 Genome sequences: The reference genome of SARS-CoV (RefSeq Accession no. NC_004718.3) and SARS-CoV-2 (RefSeq Accession no. NC_045512.2) was fetched from NCBI RefSeq database (NCBI-RefSeq, 2020).	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   2.6 Target genes functional enrichment analysis: 2.7 Microarray expression data analysis: Microarray data for change in gene expression induced by SARS-CoV on 2B4 cells infected with SARS-CoV or remained uninfected for 12, 24, and 48hrs obtained from Gene Expression Omnibus (	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   ) (version 3.2.4 under Bioconductor version 3.10; R version 3.6.0).	Bioconductor suggested: (Bioconductor, RRID:SCR_006442)
   To determine genes that are differentially expressed (DE) between two experimental conditions, Bioconductor package Limma (Smyth, 2005) was utilized to generate contrast matrices and fit the corresponding linear model.	Limma suggested: (LIMMA, RRID:SCR_010943)
   Probe annotations to genes were done using the Ensembl gene model (Ensembl version 99) as extracted from Biomart (Flicek et al., 2007) and using in-house python script.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   For differential expression (DE) analysis we used Bioconductor package DESeq2 (version 1.38.0) (Anders and Huber, 2010) with R version 3.6.0 (Team, 1999) with a model based on the negative binomial distribution.	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   To avoid false positive, we considered only those transcripts where at least 10 reads are annotated and a p-value of 0.01. 2.9 MicroRNA Clustering: The hierarchal clustering of human miRNAs that could target SARS-CoV-2 genomes (binary mode) obtained from various countries was done using Manhattan distance and complete linkage analysis with the Genesis tool (Sturn et al., 2002).	Genesis suggested: (Genesis, RRID:SCR_015775)

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.05.06.081026v1 on bioRxiv

   May 8, 2020