Differential interferon-α subtype immune signatures suppress SARS-CoV-2 infection

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   ScreenIT

   May 22, 2021

   SciScore for 10.1101/2021.05.20.444757: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Then, the blocking buffer was aspirated and 50 μl of primary antibody solution (anti-SARS-CoV-2-NP (RRID: AB_2890255) 1:5000 diluted in PBS + 1% FBS) was added to each well.	anti-SARS-CoV-2-NP detected: (Antibodies-Online Cat# ABIN6952435, RRID:AB_2890255)
   Thereafter, 50 μl of the secondary antibody solution (Peroxidase-AffiniPure Goat Anti-Mouse IgG (H+L) (RRID: AB_10015289) 1:2000 in PBS, 1% FBS) was added to the wells and the plate was incubated for 2 h at room temperature.	Anti-Mouse …

   SciScore for 10.1101/2021.05.20.444757: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Then, the blocking buffer was aspirated and 50 μl of primary antibody solution (anti-SARS-CoV-2-NP (RRID: AB_2890255) 1:5000 diluted in PBS + 1% FBS) was added to each well.	anti-SARS-CoV-2-NP detected: (Antibodies-Online Cat# ABIN6952435, RRID:AB_2890255)
   Thereafter, 50 μl of the secondary antibody solution (Peroxidase-AffiniPure Goat Anti-Mouse IgG (H+L) (RRID: AB_10015289) 1:2000 in PBS, 1% FBS) was added to the wells and the plate was incubated for 2 h at room temperature.	Anti-Mouse IgG detected: (Jackson ImmunoResearch Labs Cat# 115-035-003, RRID:AB_10015289)
   After incubation with the primary antibody solution, 50 μl secondary antibody solution (Goat IgG anti-Mouse IgG (H+L)-Alexa Fluor 488, MinX none 1:2000 (RRID: AB_2338840), Phalloidin CF647 1:100 (Biotium) in PBS + 1% FBS) were added to each well and the plate was incubated for 2 h at room temperature.	anti-Mouse IgG detected: (Jackson ImmunoResearch Labs Cat# 115-545-003, RRID:AB_2338840)
   Experimental Models: Cell Lines
   Sentences	Resources
   End-point dilution assay: VeroE6 cells were seeded at a density of 10,000 cells per well in a 96-well plate and maintained in 200 μl DMEM (Gibco) supplemented with 10% fetal bovine serum (Sigma-Aldrich), L-glutamine (Gibco), penicillin and streptomycin (Gibco) overnight.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   IAV plaque assay: MDCK-II cells were seeded in 6 well plates, and cultured in DMEM supplemented with 5% FBS and 1% Penicillin-Streptomycin until 100% confluent.	MDCK-II suggested: None
   Recombinant DNA
   Sentences	Resources
   To assess M- and N-gene copy numbers, the M- and N-gene were partially cloned into pCR™2.1 (ThermoFisher Scientific) or pMiniT 2.0 (NEB), respectively, and a 1:10 plasmid dilution series was used as a reference.	pCR™2.1 suggested: None
   Software and Algorithms
   Sentences	Resources
   The inhibitory concentration 50 (IC50) was calculated using GraphPad Prism 6.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   The 10 highest abundant peptide ions were fragmented by HCD (NCE [normalized collision energy] = 27) and MS/MS spectra were acquired at a resolution of 35,000. Proteomics Data Analysis: Peptide identification and quantification were performed using MaxQuant (v.1.6.17) searching UniProtKB/SwissProt (2020_05, 563,552 entries) restricted to either Homo sapiens or Homo sapiens and SARS-CoV-2.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485)
   GO annotation and enrichment analyses were performed using STRING (v.11).	STRING suggested: (STRING, RRID:SCR_005223)
   Data visualization was done using R and Cytoscape (v.3.8.2).	Cytoscape suggested: (Cytoscape, RRID:SCR_003032)
   The mass spectrometry proteomics data have been deposited at the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD000XXX.	ProteomeXchange suggested: (ProteomeXchange, RRID:SCR_004055) PRIDE suggested: (Pride-asap, RRID:SCR_012052)
   Transcriptomics: Quality and integrity of total RNA was controlled on 5200 Fragment Analyzer System (Agilent Technologies)).	Agilent Technologies suggested: (Agilent Technologies, RRID:SCR_013575)
   All FASTQ files were aligned to the gene model Ensembl v96 and to the reference library Human B38 using the proprietary OmicSoft Aligner OSA62.	Ensembl suggested: (Ensembl, RRID:SCR_002344)
   Differentially expressed genes were sent to Ingenuity Pathway Analysis (IPA) (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/) for biological analysis using the cutoffs: p-value <0.05, fold change (fc) >|1.5| and mean counts min>5.	Ingenuity Pathway Analysis suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)
   Statistical analysis: Differences in transformed data were tested for significance using GraphPad Prism v8.4.2 for Windows (GraphPad).	GraphPad 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 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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   Results from scite Reference Check: We found no unreliable references.

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2. 

   Version published to 10.1101/2021.05.20.444757v1 on bioRxiv

   May 20, 2021