Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

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1. Version published to 10.1016/j.cell.2020.08.001

   Sep 1, 2020
2. 

   ScreenIT

   Jun 10, 2020

   SciScore for 10.1101/2020.06.03.20119818: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	The resulting flow cytometry standard (FCS) files were normalized and randomized using the CyTOF software’s internal FCS-Processing module on the non-randomized (‘original’) data.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Study subjects: Antibodies used for mass cytometry: All anti-human antibodies pre-conjugated to metal isotopes were obtained from Fluidigm Corporation (San Francisco, US).	anti-human suggested: None
   For barcoding antibodies recognising human beta-2 microglobulin (B2M) were conjugated in house to 104Pd, 106Pd, 108Pd, 110Pd, 198Pt …

   SciScore for 10.1101/2020.06.03.20119818: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	The resulting flow cytometry standard (FCS) files were normalized and randomized using the CyTOF software’s internal FCS-Processing module on the non-randomized (‘original’) data.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Study subjects: Antibodies used for mass cytometry: All anti-human antibodies pre-conjugated to metal isotopes were obtained from Fluidigm Corporation (San Francisco, US).	anti-human suggested: None
   For barcoding antibodies recognising human beta-2 microglobulin (B2M) were conjugated in house to 104Pd, 106Pd, 108Pd, 110Pd, 198Pt (Mei et al., 2015, 2016; Schulz and Mei, 2019).	B2M suggested: None
   For secondary antibody staining of panel 2, cells were washed and stained with anti-APC 163Dy for 30 min at 4°C.	anti-APC suggested: None
   Afterwards, patient samples were hashtagged with TotalSeq-A antibodies (Biolegend) according to the manufacturer’s protocol for TotalSeqTM-A antibodies and cell hashing with 10x Single Cell 3’ Reagent Kit v3.1.	TotalSeq-A suggested: None TotalSeqTM-A suggested: None
   Software and Algorithms
   Sentences	Resources
   Libraries were quantified by Qubit™ 2.0 Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent).	Qubit™ suggested: None
   Then, STAR 2.6.1b was used for alignment against the Gencode v33 (GRCh38.p13) reference genome. dropseq-tools 2.0.0 were used to quantify gene expression and collapse to UMI count data.	STAR suggested: (STAR, RRID:SCR_015899)
   ScRNA-seq data analysis of Rhapsody data of cohort 2: Mass cytometry data analysis: Cytobank.org was used for de-barcoding of individual samples and manually gating of cell events to remove doublets, normalization beads and dead cells (Kotecha et al., 2010).	Cytobank suggested: (Cytobank, RRID:SCR_014043)

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   Results from OddPub: Thank you for sharing your data.

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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: Please consider improving the rainbow (“jet”) colormap(s) used on page 60. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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.
   • Thank you for including a protocol registration statement.

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3. 

   Version published to 10.1101/2020.06.03.20119818 on medRxiv

   Jun 5, 2020