Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19
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SciScore for 10.1101/2020.06.12.148916: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Cells were stimulated by the addition of individual virus-specific peptide pools (1 µg/ml) for 6 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). CD40suggested: NoneFor subsequent MACS-based enrichment of CD154+, cells were sequentially stained with fluorescence-labeled surface antibodies (antibody list in Table S2), Cell-hashtag TotalSeq(tm)-C antibody (0.5 µg/condition), and a biotin-conjugated CD154 antibody (clone 5C8; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec) CD154suggested: Noneanti-biotin microbeads ( Miltenyi Biotec)suggested: NoneAnalogous to … SciScore for 10.1101/2020.06.12.148916: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Cells were stimulated by the addition of individual virus-specific peptide pools (1 µg/ml) for 6 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). CD40suggested: NoneFor subsequent MACS-based enrichment of CD154+, cells were sequentially stained with fluorescence-labeled surface antibodies (antibody list in Table S2), Cell-hashtag TotalSeq(tm)-C antibody (0.5 µg/condition), and a biotin-conjugated CD154 antibody (clone 5C8; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec) CD154suggested: Noneanti-biotin microbeads ( Miltenyi Biotec)suggested: NoneAnalogous to enrichment for CD154+, CD137-expressing CD4+ memory T cells cells were positively selected by staining with biotin-conjugated CD137 antibody (clone REA765; Miltenyi Biotec) followed by anti-biotin MicroBeads and applied to a new MS column. CD137suggested: Noneanti-biotinsuggested: NoneSoftware and Algorithms Sentences Resources All flow cytometry data were analyzed using FlowJo software (version 10). FlowJosuggested: (FlowJo, RRID:SCR_008520)The merged data was transferred to the R statistical environment for analysis using the package Seurat (v3.1.5) (Stuart et al., 2019). Seuratsuggested: (SEURAT, RRID:SCR_007322)Single-cell differential gene expression analysis: Pairwise single-cell differential gene expression analysis was performed using the MAST package in R (v1.8.2) (Finak et al., 2015) after conversion of data to log2 counts per million (log2 CPM + 1). MASTsuggested: (MAST, RRID:SCR_016340)Results from OddPub: Thank you for sharing your code.
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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