Prism program

Manufactured by GraphPad

Sourced in United States

GraphPad Prism is a data analysis and graph creation software package. It provides a wide range of statistical and graphical tools to help researchers analyze, visualize, and present their data.

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Lab products found in correlation

Spss version 22, by IBM (2 mentions) Blitz system, by Molecular Devices (2 mentions) Spectrostar nano, by BMG Labtech (2 mentions) Eclipse te2000 u inverted fluorescence microscope, by Nikon (1 mentions) Paclitaxel, by Teva Pharmaceuticals (1 mentions) Wallac victor2 1420 multilabel counter, by PerkinElmer (1 mentions) Celltiter 96 aqueous non radioactive cell proliferation assay, by Promega (1 mentions) Stata, by StataCorp (1 mentions) Statistical package for social sciences spss version 23, by IBM (1 mentions) Spss for mac ver 20, by IBM (1 mentions) Statistica 12, by TIBCO Software (1 mentions) Damgo, by PerkinElmer (1 mentions) Damgo, by Merck Group (1 mentions) Prism 8, by GraphPad (1 mentions) Hl 60mx2, by American Type Culture Collection (1 mentions) Rpmi 1640, by Thermo Fisher Scientific (1 mentions) Penicillin streptomycin, by Thermo Fisher Scientific (1 mentions) Celltiter blue cell viability assay kit, by Promega (1 mentions) Spss software, by IBM (1 mentions) Spss 19.0 statistical package, by IBM (1 mentions)

135 protocols using prism program

Animal Characterization, Glycogen, and Metabolic Studies

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Animal characterization studies, glycogen content and serum biochemistry were analyzed by unpaired t-tests using the GraphPad Prism Program, version 7 (GraphPad Software Inc., San Diego, CA, USA). For gene expression studies, the normality of the mRNA expression data was first examined. As some gene expression data deviate from normality, Wilcoxon Rank Sum Tests were performed, using SAS version 9.4 (SAS, Inc., Cary, NC, USA) to validate initial analyses by unpaired t-tests using GraphPad Prism Program, version 7 (GraphPad Software Inc., San Diego, CA, USA). All tests were two-sided and values of p < 0.05 were considered statistically significant. For metabolic studies, relative change in glucose levels (to baseline) was plotted using GraphPad Prism Program, version 7 (GraphPad Software Inc., San Diego, CA, USA).

Arends C.J., Wilson L.H., Estrella A., Kwon O.S., Weinstein D.A, & Lee Y.M. (2022). A Mouse Model of Glycogen Storage Disease Type IX-Beta: A Role for Phkb in Glycogenolysis. International Journal of Molecular Sciences, 23(17), 9944.

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Statistical Analysis of Experimental Data

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Statistical analysis was performed using the GraphPad Prism Program version 5.02. Due to the small sample size, normality of the data was checked through the Kolmogorov-Smirnov test that employs a Dallal and Wilkinson approximation to the Lilliefors' method. Equality of variance of the samples was verified using the Bartlett's test. A one-way analysis of variance (ANOVA) was used if the data were found to be normally distributed and homogeneous. The Bonferroni's multiple comparison post hoc test was then used to compare differences between sample dates. However, if the data did not meet the requirements for normal distribution, the Kruskal-Wallis (KW) one-way ANOVA on ranks was performed to compensate, and the Dunn's post hoc test was employed to compare differences between sample dates. If significant differences in variance based on the Bartlett's test were found, the data was log transformed and a one-way ANOVA was performed. If the Bartlett's test on the transformed data was significant, the variances were considered unequal and a KW ANOVA was performed; otherwise, the one-way ANOVA was reported. If an ANOVA was performed, the p value of the original Bartlett's test was still reported and the variance described. Statistical significance was defined as p ≤ 0.05.

Rougée L.R., Richmond R.H, & Collier A.C. (2015). Molecular reproductive characteristics of the reef coral Pocillopora damicornis. Comparative biochemistry and physiology. Part A, Molecular & integrative physiology, 189, 38-44.

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Statistical Analysis of Activation Assay

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Statistical analysis of activation assay samples was performed using one-way ANOVA Friedman test with Dunn post-test (Prism Program; Graphpad software, La Jolla, USA). In the graphs p values are indicated as follows: * p<0.05; ** p<0.01; *** p<0.0001; n.s. not significant (p>0.05). For statistical analysis of experiments with only two groups, the Wilcoxon signed ranks test was used for paired samples whereas the Mann-Whitney U test was used for unpaired samples. To determine correlations between cytokine levels in ascites and suppression, the distribution of variables was assessed by D’Agostino and Pearson omnibus normality test. Where cytokine levels in ascites samples were distributed normally, correlation to suppression was assessed by calculating the Pearson coefficient using Prism Software. For cytokine levels lacking normal distribution across ascites samples, the Spearman coefficient was calculated instead.

Brencicova E., Jagger A.L., Evans H.G., Georgouli M., Laios A., Attard Montalto S., Mehra G., Spencer J., Ahmed A.A., Raju-Kankipati S., Taams L.S, & Diebold S.S. (2017). Interleukin-10 and prostaglandin E2 have complementary but distinct suppressive effects on Toll-like receptor-mediated dendritic cell activation in ovarian carcinoma. PLoS ONE, 12(4), e0175712.

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Cytotoxicity Evaluation of Anticancer Drugs

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Cytotoxicity was determined using MTT and colony formation assays as previously described (2 (link),16 (link)). MTT assay was used to determine cytotoxicity of anticancer drugs. Briefly, cells were seeded in 96-well plate at 3000 cells/well and cultured for 24 hrs followed by treatment with anticancer drugs and cultured continuously for 72 hrs at 37°C. Then, MTT (5 mg/mL) was added to the culture and incubated for another 4 hrs. The culture medium was then aspirated followed by addition of DMSO and absorption was determined using a 96-well plate reader. For colony formation assay, 100–200 cells/well were seeded in 6-well plate and cultured for 24 hrs before IR treatment. The cells were then cultured for 10 days before fixation and staining with crystal violent (0.005% in 20% methanol). The colonies were counted manually. Both the fitted sigmoidal dose response curve and IC₅₀ were calculated using Graph Pad Prism Program.

Chen Y., Li Z., Dong Z., Beebe J., Yang K., Fu L, & Zhang J.T. (2017). 14-3-3σ Contributes to Radioresistance by Regulating DNA Repair and Cell Cycle via PARP1 and CHK2. Molecular cancer research : MCR, 15(4), 418-428.

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Wound Healing Assay of HRMECs

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Primary HRMECs were seeded in six-well plates (5 × 10⁴ cells/well), incubated in complete classic medium with supplements included in the media kit (Cell Systems) for 3 days, and then subjected to serum starvation using complete serum-free medium (CSFM) for 6 hours. Thereafter, a straight scratch was made across the layer of cultured cells using a 200-µL micropipette tip. The cells were treated with ranibizumab, aflibercept, or IDB0062 in the presence or absence of VEGFA (50 ng/mL), VEGFB (50 ng/mL), or PlGF2 (100 ng/mL) in CSFM and incubated (37°C, 5% CO₂). Images of the cells were acquired using an Eclipse TE2000-U inverted fluorescence microscope (Nikon, Tokyo, Japan) at 0 hour and at the final time point (15.5–16.5 hours). The wound area was quantitated using the MRI Wound Healing Tool of ImageJ (v1.4.3.67; National Institutes of Health, Bethesda, MA). Half-maximal inhibitory concentration (IC₅₀) was calculated using the Prism program (GraphPad, San Diego, CA).

Kim S., Min G., Kim B., Lee D., Lee M., Ko J.H, & Kwon H.S. (2021). Novel Dual-Targeting Antibody Fragment IDB0062 Overcomes Anti–Vascular Endothelial Growth Factor Drug Limitations in Age-Related Macular Degeneration. Translational Vision Science & Technology, 10(14), 35.

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Effects of Cognitive Therapy on Anxiety

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All statistics shown were conducted using Student’s t test (unless specified) on the Prism program (GraphPad Software), where *, P < 0.05; **, P < 0.01; and ***, P < 0.001. For all figures, the mean and standard error of means are represented.

Glenn J.D., Smith M.D., Xue P., Chan-Li Y., Collins S., Calabresi P.A., Horton M.R, & Whartenby K.A. (2017). CNS-targeted autoimmunity leads to increased influenza mortality in mice. The Journal of Experimental Medicine, 214(2), 297-307.

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Survival Analysis of Prostate Cancer

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Categorical variables were reported as counts and percentages; continuous variables were reported as medians and interquartile ranges (IQR). Comparisons were made using the chi-square test for categorical variables and an independent t-test for continuous variables. Kaplan–Meier survival analyses were applied for depicting OS. Inversed probability of treatment weighing-adjusted Cox proportional hazards model was performed to determine the association between various factors and OS. The optimal cutoff values for PSA nadir and TTN were calculated using receiver operating characteristic (ROC) curve analysis. All statistical analyses were performed using commercial statistical software SPSS (version 25.0; IBM Corp, SPSS, Inc, Chicago, IL, USA). Summary statistics were presented with Excel (Microsoft Office Professional Plus 2019) and PRISM program (GraphPad, V8.0.1).

Tseng C.S., Yang J.H., Huang S.W., Wang Y.J., Chen C.H., Pu Y.S., Cheng J.C, & Huang C.Y. (2023). Survival outcomes and prognostic factors for first-line abiraterone acetate or enzalutamide in patients with metastatic castration-resistant prostate cancer. BMC Cancer, 23, 568.

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Cytotoxicity Assay of Anti-Cancer Drugs

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Filtered, single-cell suspensions of monolayer and sphere cells were generated as described above for the side population assay. Cell viability was determined using the colorimetric Cell Titer 96^® Aqueous Non-Radioactive Cell Proliferation Assay (MTS assay, Promega, Madison, WI, USA) to measure cellular responses to different cytotoxic drug conditions. Each condition was performed in triplicate using 10 000 cells per well in 100 μL of culture medium. Cells were exposed to increasing concentrations of paclitaxel (TEVA Pharmaceuticals, North Wales, PA, USA) or doxorubicin (Bedford Laboratories, Bedford, OH, USA) for 72 h in 37 °C, 5% CO₂. MTS reagent was added at a ratio of 1:10 and incubated for additional 1–2 h. Absorbance (A₄₉₀) was measured using a Wallac Victor2 1420 Multilabel Counter (Perkin Elmer, Waltham, MA, USA). Cell viability was expressed as the percentage of the A₄₉₀ of drug-treated cells relative to untreated cells according to the following equation: % Viability = 100 × (A₄₉₀ drug-treated/A₄₉₀ untreated). The IC₅₀ for each drug was determined by fitting the relative viability of the cells to the drug concentration by using a dose–response model in the Prism program from GraphPad Software (San Diego, CA, USA).

Khammanivong A., Gorden B.H., Frantz A.M., Graef A.J, & Dickerson E.B. (2014). Identification of drug-resistant subpopulations in canine hemangiosarcoma. Veterinary and comparative oncology, 14(3), e113-e125.

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Kinase Selectivity Dose-Response Assay

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Kinase selectivity dose-response experiments for 31 and 33 were performed by Nanosyn (Santa-Clara, CA). Test compounds were diluted in 100% DMSO using 3-fold dilution steps. Final compound concentration in assay ranged from 10μM to 0.056 nM. Compounds were tested in a single well for each dilution, and the final concentration of DMSO in all assays was kept at 1%. All assays were performed with a substrate concentration of 1 μM and K_m ATP concentration. Enzyme concentrations ranged 0.1–2 nM, and incubation times were 2–4 hours. See Supplementary Table 11 for exact concentrations. IC₅₀ values were calculated using a sigmoidal dose response fitting in the Prism program (Graphpad) and are reported as the average of two biological experiments.

London N., Miller R.M., Krishnan S., Uchida K., Irwin J.J., Eidam O., Gibold L., Cimermančič P., Bonnet R., Shoichet B.K, & Taunton J. (2014). Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Nature chemical biology, 10(12), 1066-1072.

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Quantifying Serum Autoantibody Binding

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All samples were analysed in triplicate determinations and the intra-assay average coefficient of variation was 7%, with the highest value 20 and the lowest 0.1. The significance of differences in competition between different serum groups was tested using the non-parametric Mann–Whitney U-test. The significance of differences in binding to full-length and truncated GAD65 within the same group was tested with the paired Wilcoxon signed-rank test. The significance of correlation was analysed using Spearman’s rank correlation test. Significance of differences in frequency was tested using Fisher exact probability test. All statistical testing was two-sided, and P values <0.05 were taken to indicate statistical significance. Statistical analyses were performed using the Prism program (GraphPad, San Diego, CA, USA) and stata (stataCorp LLC, College Station, TX, USA)

Hampe C.S., Radtke J.R., Wester A., Carlsson A., Cedervall E., Jönsson B., Ivarsson S.A., Elding Larsson H., Larsson K., Lindberg B., Neiderud J., Rolandsson O, & Lernmark Å. (2018). Reduced display of conformational epitopes in the N-terminal truncated GAD65 isoform: relevance for people with stiff person syndrome or DQ8/8-positive Type 1 diabetes mellitus. Diabetic medicine : a journal of the British Diabetic Association, 36(11), 1375-1383.

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