Computational protocol: Toll-Like Receptor 4 on both Myeloid Cells and Dendritic Cells Is Required for Systemic Inflammation and Organ Damage after Hemorrhagic Shock with Tissue Trauma in Mice

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Protocol publication

[…] For flow cytometric analyses, cell suspensions of DC generated in vitro were stained with a combination of the following fluorescently conjugated monoclonal antibodies: PE-CD3 (eBioscience), FITC-CD4, APC-CD8 (eBioscience), eFlour-450 CD11c (eBioscience), PE-NK1.1 (eBioscience), APC-Cy-7-Ly6G (eBioscience), FITC-MHC II (BD Biosciences). Samples were assayed on a BD LSR II flow cytometer (BD Biosciences) and data analyzed using FlowJo software (Tree Star, Ashland, OR, USA) as previously described (). [...] The results are expressed as the mean ± SEM. All data were analyzed using SigmaPlot™ 12 software (Systat Software, Inc., San Jose, CA, USA). Statistical difference between groups was determined by either Student’s t-test, Mann–Whitney rank sum test, or two-way ANOVA as appropriate and indicated in the Figure Legends. P < 0.05 was considered statistically significant for all analyses.Dynamic Bayesian Network (DBN) inference was used to model the evolution of the probabilistic dependencies within a system over time. This analysis was carried out using MATLAB™ (The Math Works, Inc., Natick, MA, USA), using an algorithm adapted from Grzegorczyk and Husmeier () and revised by our group (, –). In this analysis, inflammatory mediators were represented at multiple time points within the same network structure. Each node (inflammatory mediator) in the network was associated with a conditional probability distribution of a variable that is conditioned upon its parents (upstream nodes). This particular network structure was used to assess the dominant inflammatory mediators and the probable interaction among various mediators, including possible feedback loops (, , ). […]

Pipeline specifications

Software tools FlowJo, SigmaPlot
Applications Miscellaneous, Flow cytometry
Organisms Mus musculus
Diseases Liver Diseases, Wounds and Injuries