Prism 8

Manufactured by GraphPad

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Prism 8 is a data analysis and graphing software developed by GraphPad. It is designed for researchers to visualize, analyze, and present scientific data.

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Lab products found in correlation

Spss 22, by IBM (232 mentions) Spss 25, by IBM (165 mentions) Spss 21, by IBM (164 mentions) Spss 26, by IBM (163 mentions) Sas 9, by SAS Institute (151 mentions) Spss 23, by IBM (133 mentions) Spss 20, by IBM (126 mentions) Spss statistics 25, by IBM (121 mentions) Spss statistics 26, by IBM (90 mentions) Spss 24, by IBM (85 mentions) Spss version 25, by IBM (85 mentions) Spss version 22, by IBM (68 mentions) Spss 19, by IBM (67 mentions) Spss statistics 20, by IBM (65 mentions) Spss statistic, by IBM (64 mentions) Sas version 9, by SAS Institute (61 mentions) Matlab, by MathWorks (61 mentions) Spss version 26, by IBM (58 mentions) Spss statistics 23, by IBM (51 mentions) Spss version 23, by IBM (47 mentions)

45 576 protocols using prism 8

Radioligand Binding and Functional Assays

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For radioligand saturation binding assays, results were analyzed using GraphPad Prism 8.4 (Graphpad Software Inc., San Diego, CA) using “One site–Total and nonspecific binding.” For the radioligand competition binding assays, data were analyzed using GraphPad Prism 8.4 (Graphpad Software Inc., San Diego, CA) using either “One site-Fit Ki” or “Two site-Fit Ki” as determined when comparing values in GraphPad Prism 8.4. For surface expression levels of WT D1R and D1R mutants, chemiluminescence values were normalized to wild-type receptor and graphed as a percentage of wild-type using GraphPad Prism 8.4 (Graphpad Software Inc., San Diego, CA). The pEC₅₀ values were calculated for individual experiments using the sigmoidal log(agonist) versus dose response function built into GraphPad Prism 8.4. Average Emax values for cAMP accumulation assay were determined from “log(agonist) vs. response-Variable slope (four parameters)” function in GraphPad Prism 8.4 software (Graphpad Software Inc., San Diego, CA). Average Emax and basal values for the β-arrestin recruitment Tango assays were determined from the highest and lowest concentrations of the respective compound. Data in the figures and tables are presented as mean values ± standard error of measurement (SEM) with the number of biological and technical replicates indicated in the figure and table legends.

Zhuang Y., Xu P., Mao C., Wang L., Krumm B., Zhou X.E., Huang S., Liu H., Cheng X., Huang X.P., Shen D.D., Xu T., Liu Y.F., Wang Y., Guo J., Jiang Y., Jiang H., Melcher K., Roth B.L., Zhang Y., Zhang C, & Xu H.E. (2021). Structural insights into the human D1 and D2 dopamine receptor signaling complexes. Cell, 184(4), 931-942.e18.

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Quantitative SARS-CoV-2 Receptor Binding Assay

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All experiments were performed with n = 3, n = 4 or n = 6 biological replicates (as indicated). Each BLI binding assay was repeated at least twice, and binding signals of representative samples were the average of technical duplicates from the same sample. Virus initial binding rates, corresponding to the slopes of the binding curves during the first 5 min, were corrected by virus particle numbers and determined by Simple linear regression (GraphPad Prism 8.4.0). Statistical significance for bar diagram plots of virus binding or entry was determined using the unpaired t-test with Welch’s correction, applying two-tailed calculation on biological replicates (n is indicated in the figure legends) (GraphPad Prism 8.4.0). Fractional receptor densities correlating with half maximum initial binding rates were determined by non-linear regression analysis and performed by the Sigmoidal, 4PL, X is log (concentration) (GraphPad Prism 8.4.0). Each luciferase biological replicate is the average of technical triplicates from the same sample. Significance analysis of luciferase reporter assay was based on one way ANOVA followed by Tukey’s multiple comparisons test (GraphPad Prism 8.4.0).

Liu M., Huang L.Z., Smits A.A., Büll C., Narimatsu Y., van Kuppeveld F.J., Clausen H., de Haan C.A, & de Vries E. (2022). Human-type sialic acid receptors contribute to avian influenza A virus binding and entry by hetero-multivalent interactions. Nature Communications, 13, 4054.

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Multivariate Analysis of qPCR Data

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Principal component analysis was performed using the online ClustVis tool (https://biit.cs.ut.ee/clustvis/) [54 (link)]. As input we have used the individual replicated qPCR expression values per sample per exposure condition.
Change in lipid accumulation in 5-dpf-old larvae was analyzed by one way ANOVA analysis using Graphpad Prism 8.
The Cq determination was done by regression and extracted from BioRad CFX Maestro software. Normalized Δ∆Cq levels were calculated, and significance analysis was performed on the log2 transformed values that were obtained via two-way ANOVA analysis with a Dunnett’s multiple comparison post hoc analysis in Graphpad Prism 8. Results are presented in a heatmap at 5 dpf (Graphpad Prism 8) using the fold change expression values.
ChIP results were analyzed by two-way ANOVA with Sidak multiple comparisons correction using Graphpad Prism 8.

den Broeder M.J., Ballangby J., Kamminga L.M., Aleström P., Legler J., Lindeman L.C, & Kamstra J.H. (2020). Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish. Epigenetics & Chromatin, 13, 5.

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Radiation Survival Curve Analysis

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Counting of γH2AX foci was determined using Image J software. For clonogenic assays, the surviving fraction was calculated on the basis of the number of colonies on non-irradiated plates. Data are presented as the log of the surviving fraction with error bars representing the SEM. Radiation survival curves were plotted in GraphPad Prism 8, using the linear-quadratic model with the equation SF = exp – (αD + βD²), where D is a dose of radiation. The FP values were plotted against the log of the protein concentrations, and the apparent dissociation constant calculated from fitting the curves with a sigmoidal four-parameter logistic binding model in GraphPad Prism 8. Spearman’s correlation value was acquired through ImageJ with colocalisation plugins, and P values for one-way ANOVA multiple comparison was calculated in GraphPad Prism 8. The levels and correlation between SPRTN and TR-MRE11 were calculated using a 2-way ANOVA multiple comparison and correlation, respectively, in GraphPad Prism 8.

Na J., Newman J.A., Then C.K., Syed J., Vendrell I., Torrecilla I., Ellermann S., Ramadan K., Fischer R, & Kiltie A.E. (2021). SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells. Cell Death & Disease, 12(2), 165.

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Statistical Analysis of Dietary Intervention Experiments

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In the dietary intervention experiments, behavioral data were analyzed in GraphPad Prism 8 using Two-Way ANOVA with Tukey’s Multiple Comparison Test. Histological data and RT-QPCR of diet brains were analyzed in GraphPad Prism 8 using one-way ANOVA with Tukey’s multiple comparison test. Differences were considered significant when p ≤ 0.05. For in vitro experiments, in vitro data were analyzed in GraphPad Prism 8 using Student’s t-test for unpaired samples (expressed as mean ± SEM; Klover assays) or one-way ANOVA with Tukey’s post hoc test for multiple comparisons among treatment groups (siRNA studies; adjusted p values from group comparisons can be found in Supplementary Table 6). The number of biological replicates was three if not otherwise stated. Differences were considered significant when p ≤ 0.05. Data from kl/kl × Wt brains were analyzed in GraphPad Prism 8 using Student’s t-test for unpaired samples (expressed as mean ± SEM). Differences were considered significant when p ≤ 0.05.

Dias G.P., Murphy T., Stangl D., Ahmet S., Morisse B., Nix A., Aimone L.J., Aimone J.B., Kuro-O M., Gage F.H, & Thuret S. (2021). Intermittent fasting enhances long-term memory consolidation, adult hippocampal neurogenesis, and expression of longevity gene Klotho. Molecular Psychiatry, 26(11), 6365-6379.

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Entomopathogenic Fungus Against Corn Borer

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The effect of the spore concentration of A. nomius ACB1041 on different life stages of O. furnacalis was compared using the “chi-squared test” functions in the “contingency table analyses” program of Graph Pad Prism 8.0. A survival analysis was conducted using the “survival curve” functions in the “survival analysis” program of Graph Pad Prism 8.0. The median lethal concentration (LC₅₀) and median lethal time (LT₅₀) were determined by conducting a probit analysis using IBM SPSS Statistics software (version 20.0.). The data of LC₅₀ and LT₅₀ values were subjected to analysis of variance (ANOVA), and differences among treatments were compared using the Tukey’s test (P > 0.05) to determine significance using IBM SPSS Statistics software (version 20.0.). The relationships between mortality and concentration and extracellular enzyme activities were analysed using the “linear regression” and “Fit spline/LOWESS” functions, respectively, in the “XY analyses” program of Graph Pad Prism 8.0. The results were considered statistically significant when p < 0.05. Data were analysed using IBM SPSS Statistics software (version 20.0.), and figures were constructed using Graph Pad Prism 8.0 (Graph Pad Prism).

Wang X., Ding X., Yuan Z., Jia Z., Fu K., Zhan F., Guo W., Zhou L., Li H., Dai J., Wang Z., Xie Y, & Yang X. (2023). Analysis of the virulence, infection process, and extracellular enzyme activities of Aspergillus nomius against the Asian corn borer, Ostrinia furnacalis guenée (Lepidoptera: Crambidae). Virulence, 14(1), 2265108.

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Statistical Analysis of Clinical and Preclinical Studies

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In the clinical study, compared with unpaired Student's t test or the Mann–Whitney U test, continuous variables are expressed as the mean or mean ± standard deviation (SD) for normally distributed data and medians for abnormally distributed data. Compared with the χ² test, categorical variables are expressed as numbers and percentages. ROC curve was generated with GraphPad Prism 8.0 (GraphPad Software, San Diego, CA, USA). Correlations between DDAH1 and other clinical indicators were estimated using Spearman's rank correlation coefficient and visualized via a heatmap generated with GraphPad Prism 8.0. For the preclinical study, all the data were reported as the mean ± standard error of mean (SEM). Statistical analysis was performed by two-way ANOVA with post hoc Dunnett's test or Student's t test for brain blood flow detection and the Morris water maze assay with GraphPad Prism 8.0. Other analyses were performed by one-way ANOVA with post hoc Dunnett's test or Student's t test with GraphPad Prism 8.0. The level of significance was considered at ∗P < 0.05 and ∗∗P < 0.01.

Gao Q., Ni P., Wang Y., Huo P., Zhang X., Wang S., Xiao F., Li Y., Feng W., Yuan J., Zhang T., Li Q., Fan B., Kan Y., Li Z., Qi Y., Xing J., Yang Z., Cheng H., Gao X., Feng X., Xue M., Liu Y., Luo Y., Lu Z, & Zhao Y. (2024). DDAH1 promotes neurogenesis and neural repair in cerebral ischemia. Acta Pharmaceutica Sinica. B, 14(5), 2097-2118.

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Radiation Survival Curve Analysis

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Data are presented as mean ± standard error of the mean (SEM). GraphPad PRISM 8 was used to plot graphs, radiation survival curves were fitted with the linear quadratic model. Surviving fractions at 2 Gy (SF2) and SER values were extrapolated from the fit of the linear quadratic model using PRISM 8. GraphPad PRISM 8 was used to perform the F-test and statistical analysis, p values < 0.05 were considered significant.

Bibby B.A., Thiruthaneeswaran N., Yang L., Pereira R.R., More E., McArt D.G., O’Reilly P., Bristow R.G., Williams K.J., Choudhury A, & West C.M. (2021). Repurposing FDA approved drugs as radiosensitizers for treating hypoxic prostate cancer. BMC Urology, 21, 96.

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Robust Statistical Analysis of Biological Data

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Statistical analyses were performed using GraphPad Prism 8 (GraphPad, San Diego, CA). All data were first tested or a Gaussian distribution using a D’Agostino-Pearson test. The statistical significance between means was determined by either parametric or non-parametric Student’s t-test, analysis of variance (ANOVA) followed by post hoc comparisons (Tukey, Sidak) using Prism 8. Statistical significance was set at α < 0.05. Error bars in the graphs represent mean ± SEM. See statistical analyses described in Table 1. All data were plotted in Prism 8.

Boinon L., Yu J., Madura C.L., Chefdeville A., Feinstein D.L., Moutal A, & Khanna R. (2022). Conditional knockout of CRMP2 in neurons, but not astrocytes, disrupts spinal nociceptive neurotransmission to control the initiation and the maintenance of chronic neuropathic pain. Pain, 163(2), e368-e381.

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Calculating IC50 and EC50 Using Prism 8

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Statistical analysis was performed with GraphPad Prism 8.0. IC 50 and EC 50 calculations and statistical analysis were performed using Prism 8.0 from GraphPad. P-values < 0.001 are statistically significant. Comparisons between two normally distributed groups were performed by Wilcoxon signed rank test using Prism 8.

Nejat R., Sadr A.S., Freitas B., Crabttree J., Pegan S.D., Tripp R.A, & Najafi D. (2021). Losartan Inhibits SARS-CoV-2 Replication in Vitro. Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques, 24.

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