Functional proteomic profiling links deficient DNA clearance with increased mortality in individuals with severe COVID-19 pneumonia
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SciScore for 10.1101/2022.01.25.22269616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Human healthy donor and clinical samples of Sepsis and COVID-19 patients: For the in vitro neutrophil experiments, peripheral blood was isolated from consenting healthy adult volunteers, according to approved protocols of the ethics board of the Francis Crick Institute and the Human Tissue act.
Consent: Written informed consent was obtained from participants or authorized representatives.
Euthanasia Agents: The mice were culled via cervical dislocation or by lethal dose of pentobarbital (600mg/kg) with mepivacaine hydrochloride (20mg/ml).Sex as a biological variable not detected. Randomization Plasma sample preparation for proteomic analysis: Healthy donor and patient plasma samples were … SciScore for 10.1101/2022.01.25.22269616: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Human healthy donor and clinical samples of Sepsis and COVID-19 patients: For the in vitro neutrophil experiments, peripheral blood was isolated from consenting healthy adult volunteers, according to approved protocols of the ethics board of the Francis Crick Institute and the Human Tissue act.
Consent: Written informed consent was obtained from participants or authorized representatives.
Euthanasia Agents: The mice were culled via cervical dislocation or by lethal dose of pentobarbital (600mg/kg) with mepivacaine hydrochloride (20mg/ml).Sex as a biological variable not detected. Randomization Plasma sample preparation for proteomic analysis: Healthy donor and patient plasma samples were randomised and plated in a 96-well plate (Eppendorf). Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources For in vivo histone neutralisation, the mice received combined anti-histone 3 (Merck Millipore; 07-690) and anti-histone 4 antibodies (Merck Millipore; 04-858) or control polyclonal rabbit IgG (BioXCell). anti-histone 3suggested: Noneanti-histone 4suggested: NoneAnti-histone antibodies were dialysed and injected intraperitoneally, starting on D-1 (200μg/mouse) and daily afterwards (200μg H3 and 100μg H4). Anti-histonesuggested: NoneSamples were then stained overnight in a dark humified chamber with the following primary antibodies in blocking buffer: anti-mouseCD3 (BioLegend; clone 17A2), anti-CD3 (Abcam; ab5690), anti-CD169 (BioLegend; clone 3D6.112) and anti-MPO (R&D Systems; AF3667). anti-mouseCD3suggested: Noneanti-CD3suggested: (Abcam Cat# ab5690, RRID:AB_305055)anti-CD169suggested: Noneanti-MPOsuggested: NoneFor secondary staining, tissues were stained for 2hrs in a humidified dark chamber at RT with the following labelled secondary antibodies in blocking buffer: donkey anti-rabbit IgG (Invitrogen) and donkey anti-goat IgG (Invitrogen). anti-rabbit IgGsuggested: Noneanti-goat IgGsuggested: NoneActin was detected with anti-actin (Milipore) and HRP– conjugated donkey anti-mouse (Thermo Scientific) antibodies. anti-actinsuggested: Noneanti-mousesuggested: NoneExperimental Models: Organisms/Strains Sentences Resources All experiments were conducted with age-matched and cage-controlled, 8 to 12-week-old female WT C57BL/6J and TCRα-/- (Tcratm1Phi) mice, according to local guidelines and UK Home Office regulations under the Animals Scientific Procedures Act 1986 (ASPA). C57BL/6Jsuggested: NoneSoftware and Algorithms Sentences Resources Samples were then stained overnight in a dark humified chamber with the following primary antibodies in blocking buffer: anti-mouseCD3 (BioLegend; clone 17A2), anti-CD3 (Abcam; ab5690), anti-CD169 (BioLegend; clone 3D6.112) and anti-MPO (R&D Systems; AF3667). BioLegendsuggested: (BioLegend, RRID:SCR_001134)Images were taken using the Leica TCS SP5 inverted confocal microscope (20x, 40x, 63x original magnification) and analysis was performed using Fiji/ImageJ version 2.0.0 software. Fiji/ImageJsuggested: NoneThe images acquired from the gel were then analysis using Fiji. Fijisuggested: (Fiji, RRID:SCR_002285)Correlation and statistical analysis: All correlation and fitting analysis were performed using GraphPad Prism software aided by sorting and grouping samples using Microsoft Excel. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Thresholds for identifying and grouping patients into groups were determined using frequency analysis in Excel. Excelsuggested: NoneResults 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).
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.
Results from scite Reference Check: We found no unreliable references.
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