Deciphering the link between Diabetes mellitus and SARS-CoV-2 infection through differential targeting of microRNAs in the human pancreas

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1. Version published to 10.1007/s40618-021-01693-3

   Oct 20, 2021
2. 

   ScreenIT

   Apr 3, 2021

   SciScore for 10.1101/2021.03.31.437823: (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

   Software and Algorithms
   Sentences	Resources
   For the study, three mock-infected and three SARS-CoV-2-infected hESC pancreatic tissue samples were chosen from the Gene Expression Omnibus (GEO) dataset accession, GSE151803 [19].	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   The Differentially Expressed Genes (DEGs) between the mock-infected and the SARS-CoV-2-infected pancreatic tissue were obtained using the DESeq2 R package (padj < 0.05 and |log2FC| > 1) [20, 21].	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   Disease enrichment analysis: DEGs-based disease enrichment analysis was done through DAVID – …

   SciScore for 10.1101/2021.03.31.437823: (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

   Software and Algorithms
   Sentences	Resources
   For the study, three mock-infected and three SARS-CoV-2-infected hESC pancreatic tissue samples were chosen from the Gene Expression Omnibus (GEO) dataset accession, GSE151803 [19].	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   The Differentially Expressed Genes (DEGs) between the mock-infected and the SARS-CoV-2-infected pancreatic tissue were obtained using the DESeq2 R package (padj < 0.05 and |log2FC| > 1) [20, 21].	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   Disease enrichment analysis: DEGs-based disease enrichment analysis was done through DAVID – Functional Annotation Tool considering the Gene-Disease Associations Dataset (GAD) [22, 23].	DAVID suggested: (DAVID, RRID:SCR_001881)
   Differentially targeting miRNAs: The complete genome reference sequence of SARS-CoV-2, Wuhan-Hu-1, was retrieved from NCBI RefSeq ID, NC_045512.2 [28].	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   The human miRNAs targeting the 3’ and 5’ UTR of the SARS-CoV-2 genome (CoV-tar-miRNAs) were obtained using the miRDB online tool [29, 30].	miRDB suggested: (miRDB, RRID:SCR_010848)
   The target genes of CoV-tar-miRNAs were obtained using the Predicted Target Module of miRWalk 2.0 [31, 32].	miRWalk suggested: (miRWalk, RRID:SCR_016509)

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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 10.1101/2021.03.31.437823v1 on bioRxiv

   Mar 31, 2021