Prism v5.0b

Manufactured by GraphPad

Sourced in United States

Prism v5.0b is a data analysis and graphing software developed by GraphPad. It is designed to help researchers and scientists visualize and analyze their data. The software provides a range of tools for creating high-quality graphs and performing statistical analysis on experimental data.

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Lab products found in correlation

Creative suite, by Adobe (2 mentions) Stata 11, by StataCorp (1 mentions) Fv1000 confocal microscope, by Olympus (1 mentions) Hgu133 plus 2.0 microarrays, by Thermo Fisher Scientific (1 mentions) Spss statistic, by IBM (1 mentions)

23 protocols using prism v5.0b

Statistical Significance Analysis Protocol

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Statistical significance was analyzed with GraphPad Prism v5.0b software (GraphPad Inc.) using Student's t-test. A P value≤0.05 was considered significant. For densitometry of bands obtained in western blots, we used ImageJ software (National Institutes of Health of USA [http://imagej.nih.gov/ij/]).

Quereda J.J., Ortega Á.D., Pucciarelli M.G, & García-del Portillo F. (2014). The Listeria Small RNA Rli27 Regulates a Cell Wall Protein inside Eukaryotic Cells by Targeting a Long 5′-UTR Variant. PLoS Genetics, 10(10), e1004765.

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Aquatic Ecosystem Assessment Protocol

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Results are shown as mean ± standard error of the mean (mean ± SEM). After assessing homogeneity of variance and normality, statistical analysis of the data was carried out using one-way analysis of variance followed by the Tukey test. A comparison of triplicate tanks for all parameters was also performed with one-way analysis of variance. The level of significance was set at p < 0.05. All tests were performed using GRAPHPAD PRISM (v.5.0b) software for Macintosh.

Perera E., Sánchez-Ruiz D., Sáez M.I., Galafat A., Barany A., Fernández-Castro M., Vizcaíno A.J., Fuentes J., Martínez T.F., Mancera J.M., Alarcón F.J, & Martos-Sitcha J.A. (2020). Low dietary inclusion of nutraceuticals from microalgae improves feed efficiency and modifies intermediary metabolisms in gilthead sea bream (Sparus aurata). Scientific Reports, 10, 18676.

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Statistical Analysis of Continuous Variables

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Pairwise comparisons between groups in continuous variables were assessed with Wilcoxon ranksum tests. Correlations were examined using Spearman’s rank correlation. These analyses were performed using Stata 11.0 (StataCorp LP, College Station, TX) and GraphPad Prism v5.0b (GraphPad Software, Inc., La Jolla, CA). Adjusted differences were compared between groups with multivariable linear regression, transforming variables as appropriate to satisfy model assumptions.

Somsouk M., Estes J.D., Deleage C., Dunham R.M., Albright R., Inadomi J.M., Martin J.N., Deeks S.G., McCune J.M, & Hunt P.W. (2015). Gut epithelial barrier and systemic inflammation during chronic HIV infection. AIDS (London, England), 29(1), 43-51.

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Rotarod Evaluation of Mice

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Mice from different litters were randomly assigned for rotarod evaluation. The mice were handled under the same conditions by one investigator at the same day and time. The female44 (link) experimenter was blind as to the genotype and treatment of the mice. The mice were tested every 4 weeks, in three rotarod trials per session, allowing at least 5 min of rest between each trial. The rotarod (Ugo Basile) accelerated from 5 to 40 r.p.m. and each trial lasted 5 min. The three values were averaged, and the data were analysed using two-way ANOVA (treatment × genotype) using GraphPad Prism v.5.0b (GraphPad, San Diego, CA).

Benraiss A., Wang S., Herrlinger S., Li X., Chandler-Militello D., Mauceri J., Burm H.B., Toner M., Osipovitch M., Jim Xu Q., Ding F., Wang F., Kang N., Kang J., Curtin P.C., Brunner D., Windrem M.S., Munoz-Sanjuan I., Nedergaard M, & Goldman S.A. (2016). Human glia can both induce and rescue aspects of disease phenotype in Huntington disease. Nature Communications, 7, 11758.

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Quantitative Image Analysis Protocol

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Software (ImageJ, v. 1.45s; National Institutes of Health; Bethesda, MD: http://imagej.nih.gov/ij) was used to measure the bands from both the Western blot and the RT-PCR data (n=3), and to count the number of Ki67-positive cells and nuclei stained with DAPI (n=4). The data was plotted and analyzed for significant variations (p<0.05) using the Student’s t-test and Dunnett’s Multiple Comparison test (GraphPad Prism v.5.0b; La Jolla, CA).

Guo X., Hutcheon A.E., Tran J.A, & Zieske J.D. (2017). TGF-β-target genes are differentially regulated in corneal epithelial cells and fibroblasts. New frontiers in ophthalmology (London), 3(1), 10.15761/NFO.1000151.

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Analytical Techniques for AAIL Samples

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The proton nuclear magnetic resonance (¹H NMR) data of AAIL samples were analyzed using MestReNova LITE 9.0.1, and Fourier transform infrared spectroscopy (FT-IR) data were analyzed by OriginLab 8.0 (OriginLab Corporation, American). Toxic and biodegradable data were analyzed using the graphics program GraphPad Prism v5.0b (GraphPad Software Inc.). All data are presented as the mean of three independent experiments with error values expressed as the standard error of the mean (SEM).

Wu S., Li F., Zeng L., Wang C., Yang Y, & Tan Z. (2019). Assessment of the toxicity and biodegradation of amino acid-based ionic liquids. RSC Advances, 9(18), 10100-10108.

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Bioinformatic Analysis of Regeneration Genes

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All bioinformatics processing and analyses were performed using the Lumenogix Bioinformatics-in-a-Box web platform (Umylny & Weisburd, 2011 ) and GO term overrepresentation analysis was performed using the Panther database (www.pantherdb.org; Mi et al., 2013 (link)). Venn diagrams were created using the online tool GeneVenn (genevenn.sourceforge.net; RRID:SCR_012117). Heat maps were constructed and clustering was performed using the Broad Institute’s Morpheus tool (https://software.broadinstitute.org/morpheus; RRID:SCR_017386), available online. For analysis of regeneration-associated genes (RAGs) and neurodevelopmental genes, FPKM values resulting from the cufflinks package were used to assess expression levels and gene expression heatmaps were constructed in Morpheus. All graphs were produced using GraphPad Prism v5.0b (RRID:SCR_002798). All figures were produced using the Adobe Creative Suite (RRID:SCR_010279; RRID:SCR_014199).

Wheaton B.J., Sena J., Sundararajan A., Umale P., Schilkey F, & Miller R.D. (2020). Identification of regenerative processes in neonatal spinal cord injury in the opossum (Monodelphis domestica): A transcriptomic study. The Journal of Comparative Neurology, 529(5), 969-986.

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Bioinformatics Analysis of Regeneration-Associated Genes

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All bioinformatics processing and analyses were performed using the Lumenogix Bioinformatics‐in‐a‐Box web platform (Umylny & Weisburd, 2011) and GO term overrepresentation analysis was performed using the Panther database (www.pantherdb.org; Mi et al., 2013). Venn diagrams were created using the online tool GeneVenn (genevenn.sourceforge.net; RRID:SCR_012117). Heat maps were constructed and clustering was performed using the Broad Institute's Morpheus tool (https://software.broadinstitute.org/morpheus; RRID:SCR_017386), available online. For analysis of regeneration‐associated genes (RAGs) and neurodevelopmental genes, FPKM values resulting from the cufflinks package were used to assess expression levels and gene expression heatmaps were constructed in Morpheus. All graphs were produced using GraphPad Prism v5.0b (RRID:SCR_002798). All figures were produced using the Adobe Creative Suite (RRID:SCR_010279; RRID:SCR_014199).

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In Vitro Experimental Analysis

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All in vitro experiments were repeated at least three times, and different samples were used for each experimental replicate. The results from the in vitro experiments were analyzed using one-way analysis of variance (ANOVA) or t-tests if only two conditions were being compared. All data were analyzed using Prism V.5.0b software (GraphPad Software, USA). P-values ≤ 0.05 were considered statistically significant. The results are expressed as the means ± S.D.

Miao Y., Dong Y., Huang P., Zhao X., Huang Z., Yao J., Li H, & Xu Q. (2017). Increasing UCP2 expression and decreasing NOX1/4 expression maintain chondrocyte phenotype by reducing reactive oxygen species production. Oncotarget, 8(38), 63750-63763.

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Quantifying Lipid Microdomain Dynamics

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Imaging was conducted using an Olympus FV1000 Confocal Microscope using a 60× 1.35NA oil immersion objective (Olympus, Waltham, MA). Analysis of microdomains was conducted with NIH ImageJ as previously described [46 (link);47 (link)]. After background subtraction, membrane microdomains were quantified as the area occupied by the fluorophore Texas Red DHPE, which reports on disordered microdomains [48 (link)-50 (link)]. A range of microdomain areas were measured and are presented as a frequency distribution. A Gaussian fit (Graph Pad Prism v5.0b) was applied to the frequency distributions. Larger areas reflect greater coverage of the fluorophore on the perimeter of the GUV. The diameter of each GUV was quantified using NIH ImageJ.

Pennington E.R., Fix A., Sullivan E.M., Brown D.A., Kennedy A, & Shaikh S.R. (2016). Distinct membrane properties are differentially influenced by cardiolipin content and acyl chain composition in biomimetic membranes. Biochimica et biophysica acta, 1859(2), 257-267.

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