Major alterations in the mononuclear phagocyte landscape associated with COVID-19 severity

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.08.25.20181404: (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.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Briefly, 50 μl EDTA blood and 20 μl of antibody mix (6-color TBNK Reagent and CD123 BUV395 from BD, CD15 PB, CD193 BV605 and HLA-DR BV785 from Biolegend and CD14 PE-Cy5 from eBioscience) were added in BD trucount tubes and incubated for 15 min at room temperature in the dark.	CD123 suggested: (BioLegend Cat# 306032, RRID:AB_2566448) CD193 suggested: (BD Biosciences Cat# 564188, RRID:AB_2738655) HLA-DR BV785 suggested: (BioLegend Cat# 307641, RRID:AB_2561360) CD14 suggested: None
   …

   SciScore for 10.1101/2020.08.25.20181404: (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.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Briefly, 50 μl EDTA blood and 20 μl of antibody mix (6-color TBNK Reagent and CD123 BUV395 from BD, CD15 PB, CD193 BV605 and HLA-DR BV785 from Biolegend and CD14 PE-Cy5 from eBioscience) were added in BD trucount tubes and incubated for 15 min at room temperature in the dark.	CD123 suggested: (BioLegend Cat# 306032, RRID:AB_2566448) CD193 suggested: (BD Biosciences Cat# 564188, RRID:AB_2738655) HLA-DR BV785 suggested: (BioLegend Cat# 307641, RRID:AB_2561360) CD14 suggested: None
   Software and Algorithms
   Sentences	Resources
   Flow cytometry analysis: Acquired data was analyzed using DIVA (BD Biosciences), FlowJo v.10.5.3 (BD Biosciences) and Prism v.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   8.0.2 (GraphPad Software Inc.)	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Algorithms used for dimensionality reduction were UMAP (Becht et al., Nature Biotechnology, 2018; https://github.com/lmcinnes/umap) and Phenograph (Levine et al., Cell, 2015;	Phenograph suggested: (Phenograph, RRID:SCR_016919)
   Single cell analysis: Seurat version 3 was used to re-analyze single cell data.	Seurat suggested: (SEURAT, RRID:SCR_007322)
   In brief, scRNA-seq from previously published report22 was used and 10X Genomics filtered_feature_bc_matrix files were acquired from Gene Expression Omnibus (GEO; accession number GSE145926).	Gene Expression Omnibus suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)
   Ingenuity Pathway Analysis (IPA) was performed to study pathways (Content version: 51963813; Release Date: 2020-03-11; Ingenuity Systems)	Ingenuity Pathway Analysis suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)

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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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   Read the original source
2. Version published to 10.1073/pnas.2018587118

   Jan 21, 2021
3. 

   Version published to 10.1101/2020.08.25.20181404v1 on medRxiv

   Aug 31, 2020