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70 protocols using prism software v7

1

Cytokine Expression Analysis Protocol

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The data for the median levels of IFN-γ, TNF, IL-2, IL-6, and IL-17 expression were used to create a heat map and clustered using an algorithm with package in R. Hierarchical dendrograms represent the degree of relatedness among the data.
The statistical analysis was performed using the GraphPad Prism Software v.7 and the data were analyzed with the non-parametric Mann–Whitney U-test. The differences were considered statistically significant when p ≤ 0.05.
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2

Statistical Analysis Methods for Experiments

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Statistical analyses for all experiments were performed with Prism software v7 (GraphPad). In experiments comparing only two groups, non-parametric Mann-Whitney tests were used to compare the experimental group with the control group. For other experiments including 3 groups, non-parametric ANOVA tests (Kruskal-Wallis with Dunn’s correction for multiple tests) were used. Individual P values are indicated on the figures.
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3

Gene Expression Analysis by ANOVA

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GraphPad Prism Software v7 (San Diego, CA, USA) was used for data analysis. Results were presented as mean ± S.E.M. Gene expression and luciferase activities were analyzed using One-way or two-way ANOVA, followed by Tukey’s multiple comparison tests for individual comparisons when significant effects were detected. Differences were considered significant at p<0.05.
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4

Survival Monitoring of Fish Groups

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Mortality was observed through the course of seven days by counting daily the number of fish left in each group tank from LIV and PBS-injected groups. A survival curve was then plotted using the GraphPad Prism Software v7.
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5

Statistical Analysis of Biological Data

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Data were analyzed by appropriate parametric or nonparametric tests as indicated throughout the manuscript. Statistical analyses were performed using GraphPad Prism Software v7 (San Diego, CA). P < 0.05 was considered as a statistically significant difference.
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6

Statistical Analysis of Experimental Data

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Data for all experiments were analyzed with Prism Software V7 (GraphPad Software, La Jolla, CA) and JMP software (SAS Institute, Cary, NC). In Figures 1 and 4 “N” indicate number of mice per group. In Figures 2 and 3 “N” indicate number of experiments performed, using cells pooled form 2-3 animals in each experiment. Statistical significance was calculated by one-way ANOVA, paired or unpaired two-tailed Student’s t tests as described in the figure legends. A p ≤ 0.05 value was considered significant and are denoted in figures as follows: *, p < 0.05; **, p < 0.01; ***, p < 0.001. No statistical methods were used to predetermine sample size. No animal or sample was excluded from the analysis.
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7

Immunophenotyping of Immune Cells

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Data are presented as either as median with minimum and maximum values or mean ± SD. Unpaired student's t‐test or Mann‐Whitney test or Kruskal–Wallis or ANOVA with multiple comparison test was performed using graphpad prism software v7 to calculate significance. P < 0.05 was considered to be statistically significant and represented in figures as *P < 0.03, **P < 0.0021, ***P < 0.0002, ****P < 0.0001. All experiments were performed in independent replicates to calculate significance.
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8

Phospho-flow Analysis of STAT3 Activation

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For phospho-flow analysis of STAT3, gp130 KO HeLa cells20 were transfected with human gp130 wildtype or P498L mutant and simulated with a saturated concentration (100 nM) of IL-6 or IL-11 for 15 min at 37 °C before fixation with 2% paraformaldehyde for 10 min at room temperature. HeLa gp130 KO cells were derived from HeLa cells obtained from the German Collection of Microorganism and Cell Cultures GmbH (ACC 57). Cells were washed in PBS and permeabilized in ice-cold 100% methanol and incubated on ice for a minimum of 30 min. After permeabilization, cells were fluorescently barcoded using two NHS-dyes (PacificBlue, #10163, DyLight800, #46421, Thermo Scientific). Individual wells were stained with a combination of different concentrations of these dyes51 . Once barcoded, cells were pooled and stained with anti-pSTAT3Alexa488 (Biolegend #651006) used in a 1/50 dilution. Phospho-flow data was collected using CytoFlex flow cytometer using Kaluza Analysis software v1.3. During acquisition, individual populations were identified according to the barcoding pattern and pSTAT3Alexa488 MFI was quantified for all populations. MFI was plotted using Prism software v7 (GraphPad).
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9

Flow Cytometry Data Analysis

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Flow cytometry data were analyzed using FlowJo software (Tree Star).
Statistical analyses were performed using the Prism software v7 (GraphPad). Paired Wilcoxon tests were applied in all analysis to compare two groups, except for Fig. 8 D, where a paired t test was applied. Significance was retained for P < 0.05.
The software designed for analysis of imaging mass cytometry data is publicly available at https://github.com/ThomasWalter/ImageMassCytometry.
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10

Murine Mild Traumatic Brain Injury Protocol

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Values are expressed as mean ± SD. All statistical analyses were performed using PRISM software v.7 (GraphPad Software, La Jolla, CA). The MC data were analyzed using the non-parametric Mann Whitney U test. To compare sham-mTBI to mTBI mice in all other experiments (n > 6 and normal distribution), we used a two-tailed Student’s t-test. When comparing the effect of CB1-knockout vs. WT and TBI vs. Sham-TBI in these mice, we used a 2-Way ANOVA test. The difference between groups was defined as p < 0.05.
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