Obesity associated with attenuated tissue immune cell responses in COVID-19

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   ScreenIT

   Jan 20, 2022

   SciScore for 10.1101/2022.01.14.475727: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: The use of discard samples surplus to that required for clinical testing, and anonymised data review were conducted under the consent waiver granted by Leeds West NHS Research Ethics Committee (ref: 20/YH/0152). IRB: The use of discard samples surplus to that required for clinical testing, and anonymised data review were conducted under the consent waiver granted by Leeds West NHS Research Ethics Committee (ref: 20/YH/0152).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Samples were processed on a Fortessa flow cytometer (Becton Dickinson, Basel, Switzerland) …

   SciScore for 10.1101/2022.01.14.475727: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: The use of discard samples surplus to that required for clinical testing, and anonymised data review were conducted under the consent waiver granted by Leeds West NHS Research Ethics Committee (ref: 20/YH/0152). IRB: The use of discard samples surplus to that required for clinical testing, and anonymised data review were conducted under the consent waiver granted by Leeds West NHS Research Ethics Committee (ref: 20/YH/0152).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Samples were processed on a Fortessa flow cytometer (Becton Dickinson, Basel, Switzerland) and data analysed using Flowjo version 10.	Flowjo suggested: (FlowJo, RRID:SCR_008520)
   The data were acquired from Gene Expression Omnibus (GEO) database under accession codes GSE145926 and GSE155249, respectively.	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   Re-integration of structural cells, macrophages, T / NK cells, and B cells: Major cell types including structural cells, macrophages, T / NK cells, and B cells were re-clustered with Seurat (4.0.4), followed by removal of batch effect across different patients with harmony (1.0).	Seurat suggested: (SEURAT, RRID:SCR_007322)
   Gene set enrichment analysis (GSEA): clusterProfiler36 (3.18.1) was used to perform GSEA.	Gene set enrichment analysis suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
   Hallmark gene sets in msigdbr (7.4.1) and enricher function in clusterProfiler were used for gene functional annotation.	clusterProfiler suggested: (clusterProfiler, RRID:SCR_016884)
   Calculation of the cytokine module score: The module score was calculated using AddModuleScore function in Seurat with the cytokine and chemokine gene set from KEGG pathway.	KEGG suggested: (KEGG, RRID:SCR_012773)
   Briefly, the normalized counts and meta data extracted from Seurat objects were applied for the statistical analysis from CellPhoneDB in python 3.8.8.	CellPhoneDB suggested: (CellPhoneDB, RRID:SCR_017054) python suggested: (IPython, RRID:SCR_001658)
   Visualization: Plotting was performed using ggplot2 (3.3.5).	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Heatmap was generated using pheatmap (1.0.12).	pheatmap suggested: (pheatmap, RRID:SCR_016418)

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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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   Results from scite Reference Check: We found no unreliable references.

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2. 

   Version published to 10.1101/2022.01.14.475727v1 on bioRxiv

   Jan 18, 2022