For flow cytometry, mean equivalent of fluorochrome (MEF) values are reported. Results are expressed as the arithmetic mean ± standard error of the mean (SEM) for a given number of values (n). Comparisons between SLE patients and HC were performed using the Mann-Whitney U test. For data analysis involving more than two groups, the Kruskal-Wallis non-parametric ANOVA followed by Dunn’s multiple comparison test was used. The Spearman rank correlation was performed for correlation analyses. Statistics and graphs were generated using GraphPad Prism v6.00 for Windows (GraphPad Software).
Prism v6.00 for windows
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GraphPad Prism v6.00 for Windows is a data analysis and graphing software. It provides tools for statistical analysis, curve fitting, and creating publication-quality graphs.
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10 protocols using prism v6.00 for windows
1
Flow Cytometry Analysis of SLE Patients
2
Statistical Analysis of Experimental Data
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All data were presented as mean ± SEM. Data comparing two groups were analyzed by a t-test for statistical significance. Data with more than two groups were analyzed by a one-way analysis of variance (ANOVA) followed by a Holm–Sidak’s test as post hoc test in case of a statistically significant ANOVA result or a Kruskal–Wallis test in case of non-parametric data distribution with a Dunn’s post hoc test. A Shapiro–Wilk normality test was performed to identify parametric or non-parametric data distribution. Data analyses were performed using GraphPad Prism V.6.00 for Windows (GraphPad Software, La Jolla, CA, United States1 ). Statistical significance was determined at level of p ≤ 0.05.
3
Statistical Analysis of Biological Data
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Statistical analysis was performed using GraphPad Prism V6.00 for Windows (GraphPad Software Inc., La Jolla, CA, United States). All data underwent outlier detection (ROUT method, Q = 1%) and outliers were eliminated from the analysis. Differences were considered statistically significant at p < 0.05. All tests were two-tailed. When data followed a normal distribution, unpaired t-tests or two-way ANOVA (RM in case of Sholl analysis) were used where appropriate, otherwise non-parametric Mann–Whitney or Kruskal–Wallis tests were used, as stated in the Results and figure descriptions. All values are provided as mean ± SD (for normally distributed data) or median with interquartile range (for data that did not pass normality tests).
4
Flow Cytometry Analysis Protocol
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The median fluorescence intensity values are reported for expression values using flow cytometry. Results are expressed as the median and interquartile range (IQR) or arithmetic mean (s .d .) for a given number of values (n). Normality was tested using the D’Agostino and Pearson normality test or Kolmogorov–Smirnov test. Data that did not pass were analysed using a Mann–Whitney U-test or Kruskal–Wallis non-parametric analysis of variance (ANOVA) followed by Dunn’s multiple comparison test. Otherwise, a one-way ANOVA was used followed by Tukey’s multiple comparisons test to analyse three groups. For correlation analysis, a non-parametric Spearman rank correlation was determined. Statistics and graphs were generated using GraphPad Prism v6.00 for Windows (GraphPad Software, Graphpad, La Jolla, CA, USA). Fisher’s exact test was used to test for an association between SIGLEC14-null genotype and patient/control status in the R statistical language version 3.1.2.
5
Quantifying Nucleoside Analogue Cytotoxicity and Efficacy
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The cytotoxic concentration of nucleoside analogue that inhibits cell viability by 50% (CC50) and the effective concentration of nucleoside analogue that inhibits infection of cells by 50% (EC50) were calculated for each independent experiment by non-linear regression using GraphPad Prism v6.00 for Windows (GraphPad Software, San Diego, CA). Non-ambiguous values were subjected to a replicate test to calculate confidence intervals of 95% (95% CI). CC50 and EC50 values were determined for at least two independent experiments for each nucleoside analogue and a selectivity index (SI) also calculated, (SI = CC50/EC50). EC50 values for each replicate were used to perform an unpaired two-tailed t-test to determine significant differences between U937 cells expressing SAMHD1 wt or HD206-7AA mutant and THP-1 cells expressing Vpx or untransduced cells. P values of <0.005 were considered statistically significant.
6
Quantifying Vascular Calcification Scores
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All data are mean ± SD. Statistical analyses were performed with the Graphpad Prism v6.00 for Windows (GraphPad Software Inc.). Student’s t test was used to compare 2 groups and 1-way ANOVA followed by Dunnett’s test was used for more than 2 groups. VC Agatston scores were nonnormalized parameters, and logarithmic transformation of VC Agatston scores was used in correlation analysis (Pearson Correlation Analysis). Statistical significance was accepted at P less than 0.05.
7
Coronary Calcium Score Analysis
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Statistical analyses were performed with the Graphpad Prism v6.00 for Windows (GraphPad Software Inc.). Student’s t test was used to compare 2 groups and 1-way ANOVA followed by Dunnett’s test was used for more than 2 groups. VC Agatston scores were nonnormalized parameters, and logarithmic transformation of VC Agatston scores was used in correlation analysis (Pearson Correlation Analysis).
8
Statistical Analysis of Biological Data
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After confirming the normal distribution of the data, homogeneity of variance was tested by Levene’s test. All of the data are presented as means ± standard deviations (SD) and the statistical analyses were completed using the statistical software Statistical Package for the Social Sciences (SPSS version 19.0; IBM Corp., Armonk, NY, USA). A two-tailed Student’s t test was used to compare two groups and an analysis of variance test was used to compare three or more groups. Differences with a p value of < 0.05 were considered to be statistically significant. Graphs were created using GraphPad Prism v6.00 for Windows (GraphPad Software, La Jolla, CA, USA).
9
Statistical Analysis of Experimental Data
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Statistical analysis was performed using GraphPad Prism v6.00 for Windows, GraphPad Software, La Jolla, CA, USA. Comparisons between groups were performed by two-way analysis of variance (ANOVA) with repeated measures followed by Bonferroni's multiple-comparisons test. Otherwise, the Mann–Whitney U-test was used for the analysis of two unpaired groups of confocal images. Statistical significance was defined as p < 0.05.
10
Analyzing Dose-Response Curves and Signaling
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GraphPad Prism v6.00 for Windows (GraphPad Software, La Jolla, CA, USA) was used for plotting dose-response curves. Statistical analyses were performed using Anastats (Rilly sur Vienne, France). The one sample Wilcoxon signed-rank test was used to assess the statistical significance against the null hypothesis of the difference calculated between Sham and RF field condition for basal BRET, PMA potency and efficacy. P-values less than 0.05 were considered as statistically significant.
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