Environmentally-induced mdig is a major contributor to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism

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   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.01.31.429010: (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 primary antibodies include anti-mdig (Invitrogen cat.no. 39-7300), anti-SARS-CoV-2-Spike (Abcam, ab272504), anti-Furin (Abcam, ab183495), anti-TMPRSS2 (Proteintech, cat.no. 14437-1-AP), anti-Cathepsin D (Cell signaling, cat.no. 2284S), and anti-GAPDH (Cell signaling, cat.no. 2118S).	anti-mdig suggested: None anti-SARS-CoV-2-Spike suggested: None anti-Furin suggested: (Abcam Cat# ab183495, RRID:AB_2801581) anti-TMPRSS2 suggested: None anti-Cathepsin D suggested: …

   SciScore for 10.1101/2021.01.31.429010: (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 primary antibodies include anti-mdig (Invitrogen cat.no. 39-7300), anti-SARS-CoV-2-Spike (Abcam, ab272504), anti-Furin (Abcam, ab183495), anti-TMPRSS2 (Proteintech, cat.no. 14437-1-AP), anti-Cathepsin D (Cell signaling, cat.no. 2284S), and anti-GAPDH (Cell signaling, cat.no. 2118S).	anti-mdig suggested: None anti-SARS-CoV-2-Spike suggested: None anti-Furin suggested: (Abcam Cat# ab183495, RRID:AB_2801581) anti-TMPRSS2 suggested: None anti-Cathepsin D suggested: None anti-GAPDH suggested: None
   Chromatin immunoprecipitation-sequencing (ChIP-seq): Ten million WT or KO Beas-2B cells were fixed and subjected to ChIP with ChIP-grade antibodies against H3K9me3, H3K27me3, and H3K4me3 (Active Motif, CA)	H3K9me3 suggested: None H3K27me3 suggested: None H3K4me3 suggested: None
   To block nonspecific binding of immunoglobulin, slides were incubated with a solution containing 5% goat serum, 0.2% Triton X-100 in PBS for 2 h at room temperature, followed by incubation with primary antibodies against mdig (mouse anti-MINA, Invitrogen with 1:50 dilution) overnight at 4 °C	anti-MINA suggested: None
   Goat anti-mouse biotinylated secondary antibodies were subsequently applied at 1:200 dilution and incubated for 2 h at room temperature.	anti-mouse biotinylated secondary suggested: (Millipore Cat# 21538, RRID:AB_916360)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell culture: The human bronchial epithelial BEAS-2B cells were purchased from America Type Culture Collection (	BEAS-2B suggested: BCRJ Cat# 0395, RRID:CVCL_0168)
   Software and Algorithms
   Sentences	Resources
   Gene set enrichment analyses comparing RNA-seq analyses were performed using the online public database Enrichr (http://amp.pharm.mssm.edu/Enrichr/).	http://amp.pharm.mssm.edu/Enrichr/ suggested: (Enrichr, RRID:SCR_001575)
   Pathway analyses were performed by Reactome Knowledgebase (http://www.reactome.org).	http://www.reactome.org suggested: (Reactome, RRID:SCR_003485)

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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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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
2. 

   Version published to 10.1101/2021.01.31.429010 on bioRxiv

   Feb 1, 2021