Mucosal-associated invariant T cell responses differ by sex in COVID-19
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SciScore for 10.1101/2020.12.01.407148: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics statement: This study and relevant protocols were approved by the Institutional Review Boards of Duke University Health System (DUHS) ?.
Consent: Written informed consent was obtained from all subjects or legally authorized representatives.Randomization PBMC scRNA-seq data were randomly downsampled to 50,000 cells and T and monocyte clusters were extracted based on the expression of their lineage markers. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Antibody titrations used in this study were previously established by Cytek Biosciences with slight … SciScore for 10.1101/2020.12.01.407148: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethics statement: This study and relevant protocols were approved by the Institutional Review Boards of Duke University Health System (DUHS) ?.
Consent: Written informed consent was obtained from all subjects or legally authorized representatives.Randomization PBMC scRNA-seq data were randomly downsampled to 50,000 cells and T and monocyte clusters were extracted based on the expression of their lineage markers. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Antibody titrations used in this study were previously established by Cytek Biosciences with slight modifications (see Table S2 for flow panel information). Cytek Biosciencessuggested: NoneRaw data were unmixed and further analyzed using either FlowJo for manual gating or Omiq (https://www.omiq.ai) for clustering visualization and analysis. FlowJosuggested: (FlowJo, RRID:SCR_008520)High-dimensional data analysis of flow cytometry data: Uniform Manifold Approximation and Projection (UMAP) and FlowSOM clustering analyses were performed on Omiq (https://www.omiq.ai), using equal random sampling of 3000 live CD45+ singlets. from each FCS file. FlowSOMsuggested: (FlowSOM, RRID:SCR_016899)FASTQ files were aligned with STAR aligner to the human genome reference GRCh38 from Ensemble database. STARsuggested: (STAR, RRID:SCR_015899)Inference of ligand-receptor interactions between T cells and monocytes: Ligand-receptor interactions between T cells and monocytes were inferred using CellPhoneDB (33). CellPhoneDBsuggested: (CellPhoneDB, RRID:SCR_017054)Graphical data of quantifications presented throughout are expressed as the means ± SEMs and were plotted using Graphpad Prism 8. Graphpad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Other graphs in this study were generated using either the corresponding analytic packages or R package ggplot2. ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: Thank you for sharing your data.
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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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