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Prism 7

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Prism 7.0 is a software solution designed for data analysis and visualization. It provides a comprehensive set of tools for organizing, processing, and presenting scientific data. The software is capable of handling a wide range of data formats and offers a user-friendly interface for creating high-quality graphs, charts, and plots.

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Lab products found in correlation

Simca p 12, by Sartorius (2 mentions) Agilent chrom station software, by Agilent Technologies (2 mentions) Spss statistics 19, by IBM (2 mentions) Illustrator cs6, by Adobe (2 mentions) Illustrator cs6 cc, by Adobe (1 mentions) Illustrator 6, by Adobe (1 mentions) Illustrator cc 2018, by Adobe (1 mentions) Excel 2016, by GraphPad (1 mentions) Illustrator cs6 and 2021, by Adobe (1 mentions)

13 protocols using prism 7

1

Metabolomics Data Analysis Protocol

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Statistical analysis was performed as previously described (38 (link)). Briefly, Agilent Chrom Station software (Agilent Technologies, USA) was used to analyze mass fragmentation spectrum and identify compounds thorough matching data with the National Institute of Standards and Technology (NIST) library and NIST MS search 2.0 program. The data were normalized based on total amount of correction and standardized data containing metabolites, retention times, and peak areas, and prepared for further metabolomics analysis. Significant difference of the standardized data was calculated and selected (P value <0.05) by software IBM SPSS Statistics 19. Cluster analysis was carried out by R software (R × 64 3.6.1). Normalized area of differential metabolites was analyzed with Z-score. Principal-component analysis and S-plot analysis were performed by SIMCA-P + 12.0 software (version 12; Umetrics, Umea, Sweden), and the metabolic pathway was done with MetaboAnalyst 4.0 enrichment. Interactive Pathways (iPath) analysis was conducted with iPath 3.0 (https://pathways.embl.de/). Figures were draw by GraphPad Prism 7.0 and Adobe Illustrator CS6.
Kuang S.F., Li X., Feng D.Y., Wu W.B., Li H., Peng B., Peng X.X., Chen Z.G, & Zhang T.T. (2022). Nitrite Promotes ROS Production to Potentiate Cefoperazone-Sulbactam-Mediated Elimination to Lab-Evolved and Clinical-Evolved Pseudomonas aeruginosa. Microbiology Spectrum, 10(4), e02327-21.
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2

Transcriptomic Analysis of Disease Response

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Results are presented as fold change. GO terms or KEGG pathways with q values (corrected p values) ≤0.05 were considered to be significantly enriched by candidate genes. All the figures were performed using GraphPad Prism 7.0 and Adobe Illustrator.
Zhang S., Ke Z., Yang C., Zhou P., Jiang H., Chen L., Li Y, & Li Q. (2021). High Glucose Causes Distinct Expression Patterns of Primary Human Skin Cells by RNA Sequencing. Frontiers in Endocrinology, 12, 603645.
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3

Quantitative Analysis of Protein Expression

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Data are presented as the mean ± SEM from at least three independent experiments. Unpaired Student’s t-test was used to compare normally distributed quantitative variables. p < 0.05 was considered statistically significant. All figures were designed using GraphPad Prism 7.0 and Adobe Illustrator.
Qin P., Zhou P., Huang Y., Long B., Gao R., Zhang S., Zhu B., Li Y.Q, & Li Q. (2024). Upregulation of rate-limiting enzymes in cholesterol metabolism by PKCδ mediates endothelial apoptosis in diabetic wound healing. Cell Death Discovery, 10, 263.
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4

Statistical Analyses for Biological Data

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Matlab R2016a, PASW Statistics 18.0, Prism 7.0 and Adobe Illustrator CS6/CC were used to analyze data and plot figures. Student’s t-test was used to compare two groups. Analysis of variance (ANOVA) was used to compare multiple groups. When necessary, multiple comparisons post hoc test (MCT) was used (Holm–Sidak’s test). When homogeneity was not assumed, the Kruskal–Wallis nonparametric ANOVA was selected for multiple statistical comparisons. The Mann–Whitney U test was used to determine significance between groups. Statistical data are provided in the figures. P < 0.05 was considered statistically significant.
Cavalcanti-de-Albuquerque J.P., Bober J., Zimmer M.R, & Dietrich M.O. (2019). Regulation of substrate utilization and adiposity by Agrp neurons. Nature Communications, 10, 311.
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5

Chemogenetic Manipulation Blinded Study

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Experimenters were blinded to group (alcohol or water), and chemogenetic manipulation whenever possible. Data were analyzed by ANOVAs and post-hoc tests as appropriate and indicated for each experiment. Statistical significance threshold was set at ɑ = 0.05. Statistical analysis and graph construction was performed in Graphpad Prism 7.0, and finalized figures were constructed in Adobe Illustrator and BioRender. Data are presented as Means and Standard Error of the Mean (SEM).
Dao N.C., Brockway D.F., Suresh Nair M., Sicher A.R, & Crowley N.A. (2021). Somatostatin neurons control an alcohol binge drinking prelimbic microcircuit in mice. Neuropsychopharmacology, 46(11), 1906-1917.
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6

Statistical Analysis for Comparative Studies

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A non-parametric Kruskal-Wallis one-way ANOVA was used for comparison of data sets. The Mann-Whitney U test was used for comparison between treatment conditions in collapse assays. For comparison between three or more data points a two-way ANOVA was performed, followed by a post-hoc Bonferroni correction. No statistical methods were used to predetermine sample size. Graphs and figures were produced with GraphPad Prism 7.0 and Adobe Photoshop CS6. Histograms show mean +/- s.e.m.; see Supplementary file 1 for statistical data.
Cook G.M., Sousa C., Schaeffer J., Wiles K., Jareonsettasin P., Kalyanasundaram A., Walder E., Casper C., Patel S., Chua P.W., Riboni-Verri G., Raza M., Swaddiwudhipong N., Hui A., Abdullah A., Wajed S, & Keynes R.J. (2020). Regulation of nerve growth and patterning by cell surface protein disulphide isomerase. eLife, 9, e54612.
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7

Metabolomics Data Analysis Protocol

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Statistical analysis was performed as previously described (38 (link)). Briefly, Agilent Chrom Station software (Agilent Technologies, USA) was used to analyze mass fragmentation spectrum and identify compounds thorough matching data with the National Institute of Standards and Technology (NIST) library and NIST MS search 2.0 program. The data were normalized based on total amount of correction and standardized data containing metabolites, retention times, and peak areas, and prepared for further metabolomics analysis. Significant difference of the standardized data was calculated and selected (P value <0.05) by software IBM SPSS Statistics 19. Cluster analysis was carried out by R software (R × 64 3.6.1). Normalized area of differential metabolites was analyzed with Z-score. Principal-component analysis and S-plot analysis were performed by SIMCA-P + 12.0 software (version 12; Umetrics, Umea, Sweden), and the metabolic pathway was done with MetaboAnalyst 4.0 enrichment. Interactive Pathways (iPath) analysis was conducted with iPath 3.0 (https://pathways.embl.de/). Figures were draw by GraphPad Prism 7.0 and Adobe Illustrator CS6.
Kuang S.F., Li X., Feng D.Y., Wu W.B., Li H., Peng B., Peng X.X., Chen Z.G, & Zhang T.T. (2022). Nitrite Promotes ROS Production to Potentiate Cefoperazone-Sulbactam-Mediated Elimination to Lab-Evolved and Clinical-Evolved Pseudomonas aeruginosa. Microbiology Spectrum, 10(4), e02327-21.
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8

Comparative Analysis of Experimental Treatments

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Data are presented as the mean ± SEM. Normally distributed quantitative variables were compared using Student’s t-test. Values of p < 0.05 were considered statistically significant. All figures were prepared using GraphPad Prism 7.0 and Adobe Illustrator software.
Zhou P., Yang C., Zhang S., Ke Z.X., Chen D.X., Li Y.Q, & Li Q. (2021). The Imbalance of MMP-2/TIMP-2 and MMP-9/TIMP-1 Contributes to Collagen Deposition Disorder in Diabetic Non-Injured Skin. Frontiers in Endocrinology, 12, 734485.
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9

Graphical Data Analysis of Cellular Assays

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Graphing and statistics were performed using Adobe Illustrator 6 and Prism 7. FACS analysis was performed using Flow Jo 8.7.3. Unpaired Welch’s T-tests were performed with significance level of p<0.05.
Singleton A., Khong D., Chin L.Y., Mukundan S., Li M, & Parekkadan B. (2017). An Engineered Biomarker System to Monitor and Modulate Immune Clearance of Cell Therapies. Cytotherapy, 19(12), 1537-1545.
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10

Visualizing Data with Prism and Illustrator

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Data was plotted using GraphPad Prism 7 and figures were assembled in Adobe Illustrator CC 2018 software package.
Jonsdottir H.R., Marti S., Geerts D., Rodriguez R., Thiel V, & Dijkman R. (2019). Establishment of Primary Transgenic Human Airway Epithelial Cell Cultures to Study Respiratory Virus–Host Interactions. Viruses, 11(8), 747.
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