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Prism 7 and 8

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Prism 7 and 8 are data analysis and graphing software programs developed by GraphPad. Prism is designed to help researchers visualize, analyze, and present their data. The software offers a range of features for data manipulation, statistical analysis, and graphing capabilities.

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Lab products found in correlation

Prism 7, by GraphPad (2 mentions) Originpro 9, by OriginLab (2 mentions) Microsoft excel, by GraphPad (2 mentions) Spss version 21, by IBM (1 mentions) R statistical software, by GraphPad (1 mentions) Kaluza 2, by Beckman Coulter (1 mentions) Image studio lite 5, by LI COR (1 mentions) Ensight multimode plate reader, by PerkinElmer (1 mentions) Realtime glo reagent, by Promega (1 mentions) Realtime glo mt cell viability assay, by Promega (1 mentions)

31 protocols using prism 7 and 8

1

Statistical Significance of Means

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Statistical significance of the differences between means was assessed by one-way analysis of variance (ANOVA), followed by the Student-Newman-Keuls test, to determine which groups were significantly different from the others. When only two groups had to be compared, we used the unpaired Student’s t-test. p < 0.05 was considered significant. Values are expressed as means ± standard deviation (SD). All the analyses were performed using Graph-Pad PRISM 7 and 8.
Baci D., Chirivì M., Pace V., Maiullari F., Milan M., Rampin A., Somma P., Presutti D., Garavelli S., Bruno A., Cannata S., Lanzuolo C., Gargioli C., Rizzi R, & Bearzi C. (2020). Extracellular Vesicles from Skeletal Muscle Cells Efficiently Promote Myogenesis in Induced Pluripotent Stem Cells. Cells, 9(6), 1527.
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2

Combination Therapy for Cancer

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Information on study design, sample size, number of biological replicates, number of independent experiments and statistical analysis is reported in the main text and figure legends. The survival curves of cisplatin/control ab (or cisplatin only)-, cisplatin/anti-CSF-1R- and cisplatin/anti-CSF-1R/anti-Ly6G-treated mice were repeated and confirmed in a separate animal facility (Fig. 1f, Fig. 6d-f), other in vivo interventions were performed once. In vitro experiments were repeated independently with similar results. Statistical analyses were performed using GraphPad Prism 7 and 8 (GraphPad Software Inc., La Jolla, CA). The two-tailed Mann-Whitney test was used for immunohistochemistry and flow cytometry analysis. Two-way ANOVA with Tukey’s multiple comparison test was used for the quantification of crystal violet absorbance. Two-tailed Log-Rank tests were used for Kaplan-Meier survival curves. The Fisher’s exact test (two-sided) was used for metastasis analysis. P-values <0.05 were considered statistically significant.
Salvagno C., Ciampricotti M., Tuit S., Hau C.S., van Weverwijk A., Coffelt S.B., Kersten K., Vrijland K., Kos K., Ulas T., Song J.Y., Ooi C.H., Rüttinger D., Cassier P.A., Jonkers J., Schultze J.L., Ries C.H, & de Visser K.E. (2019). Therapeutic targeting of macrophages enhances chemotherapy efficacy by unleashing type I interferon response. Nature cell biology, 21(4), 511-521.
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3

Microbial Diversity Analysis Workflow

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Alpha and beta diversity were computed using QIIME 1.9.1 (‘alpha_diversity_through_plots.py’, ‘beta_diversity_through_plots.py’ and ‘core_diversity_analyses.py’).
Statistical analyses (Mantel-Haenszel test, t test, one-way ANOVA with Tukey’s multiple comparison test, Kruskal-Wallis test with the Dunn’s multiple comparison test, as indicated in figure legends) were performed using the GraphPad Prism 7 and 8 software packages (GraphPad Software, USA).
Garland M., Hryckowian A.J., Tholen M., Oresic Bender K., Van Treuren W.W., Loscher S., Sonnenburg J.L, & Bogyo M. (2020). The Clinical Drug Ebselen Attenuates Inflammation and Promotes Microbiome Recovery in Mice after Antibiotic Treatment for CDI. Cell Reports Medicine, 1(1), 100005.
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4

Detailed Statistical Analysis Protocol

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For each analysis, groups consisting of 3 clones (three biological replicates) were analyzed. Statistical analysis and graphs were performed with the use of GraphPad Prism 7 and 8 (GraphPad Software Inc., San Diego, CA, USA). Normality distribution was analyzed with Shapiro–Wilks and D’Agostino–Pearson normality tests. Statistical significances of analyzed data were determined using the parametric or nonparametric versions of unpaired student’s t-test or ANOVA (one-way or two-way) tests, properly to obtained data set. The significance levels were set at p < 0.05 (*), p < 0.01 (**), p < 0.001 (***), and p < 0.0001 (****). All data were expressed as means ± standard deviations (SD) or ± standard of the mean (SEM) or median.
Malek N., Mrówczyńska E., Michrowska A., Mazurkiewicz E., Pavlyk I, & Mazur A.J. (2020). Knockout of ACTB and ACTG1 with CRISPR/Cas9(D10A) Technique Shows that Non-Muscle β and γ Actin Are Not Equal in Relation to Human Melanoma Cells’ Motility and Focal Adhesion Formation. International Journal of Molecular Sciences, 21(8), 2746.
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5

Chicken Embryo Developmental Assay

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Experiments were performed using chicken Gallus gallus domesticus embryos (stage HH21 (E3.5), HH34 (E8), HH36 (E10)) according to the Hamburger and Hamilton classification. The data performed on DRG were obtained from at least nine DRG in three independently performed tests. Lysates of DRG cultures were analyzed from three independent sets of samples. All statistical analysis and graphing were carried out using GraphPad Prism 7 and 8 (GraphPad Software Inc., San Diego, CA, USA). First, the normality of distribution was determined using Shapiro–Wilks test and D’ Agostino and Pearson normality tests. The parametric and nonparametric versions of statistical tests were used for normal and abnormal distributed data sets, respectively. Statistical significances were calculated with two-tailed unpaired student’s t-test or ANOVA (one-way) with posthoc test (Dunnett’s multiple comparisons test), depending on data sets and experiments. Means ± standard deviations (SD) were used for the data reporting. The significance levels were defined as p < 0.05 (*), p < 0.01 (**), p < 0.001 (***), and p < 0.0001 (****).
Mrówczyńska E, & Mazur A.J. (2021). Integrin-Linked Kinase (ILK) Plays an Important Role in the Laminin-Dependent Development of Dorsal Root Ganglia during Chicken Embryogenesis. Cells, 10(7), 1666.
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6

Combination Therapy for Cancer

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Information on study design, sample size, number of biological replicates, number of independent experiments and statistical analysis is reported in the main text and figure legends. The survival curves of cisplatin/control ab (or cisplatin only)-, cisplatin/anti-CSF-1R- and cisplatin/anti-CSF-1R/anti-Ly6G-treated mice were repeated and confirmed in a separate animal facility (Fig. 1f, Fig. 6d-f), other in vivo interventions were performed once. In vitro experiments were repeated independently with similar results. Statistical analyses were performed using GraphPad Prism 7 and 8 (GraphPad Software Inc., La Jolla, CA). The two-tailed Mann-Whitney test was used for immunohistochemistry and flow cytometry analysis. Two-way ANOVA with Tukey’s multiple comparison test was used for the quantification of crystal violet absorbance. Two-tailed Log-Rank tests were used for Kaplan-Meier survival curves. The Fisher’s exact test (two-sided) was used for metastasis analysis. P-values <0.05 were considered statistically significant.
Salvagno C., Ciampricotti M., Tuit S., Hau C.S., van Weverwijk A., Coffelt S.B., Kersten K., Vrijland K., Kos K., Ulas T., Song J.Y., Ooi C.H., Rüttinger D., Cassier P.A., Jonkers J., Schultze J.L., Ries C.H, & de Visser K.E. (2019). Therapeutic targeting of macrophages enhances chemotherapy efficacy by unleashing type I interferon response. Nature cell biology, 21(4), 511-521.
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7

Statistical Analysis of Experimental Data

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Results are expressed as mean ± standard error of the mean (SEM). Statistical analyses were tested by GraphPad Prism 7 and 8 (GraphPad Software Inc., La Jolla, CA, USA) using the unpaired student’s two-tailed t-test, the one-way ANOVA, or two-way ANOVA, followed by Tukey’s post hoc tests as appropriate. For ERG studies, two-way ANOVAs were used to gauge the effects of the genotype across stimulus intensities, and the effects at individual intensities were computed by t-tests after Holm–Bonferroni correction for the multiple comparisons. Values of p < 0.05 were considered significant.
Atawia R.T., Bunch K.L., Fouda A.Y., Lemtalsi T., Eldahshan W., Xu Z., Saul A., Elmasry K., Al-Shabrawey M., Caldwell R.B, & Caldwell R.W. (2020). Role of Arginase 2 in Murine Retinopathy Associated with Western Diet-Induced Obesity. Journal of Clinical Medicine, 9(2), 317.
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8

Quantitative Image Analysis of Cellular and Neural Responses

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Imaging data from cultured cells, acute brain slices, and transgenic flies were processed using ImageJ 1.52p software (NIH). The fluorescence response (ΔF/F0) was calculated using the formula (F–F0)/F0, in which F0 is the baseline fluorescence signal. The signal-to-noise ratio (SNR) was calculated as the peak response divided by the standard deviation of the baseline fluorescence fluctuation. The cross-correlation analyses were performed using NeuroExplorer 5 (Nex Technologies) and GraphPad Prism 7. Values with error bars indicate mean ± s.e.m.. The statistical analyses were performed using GraphPad Prism 7 and 8. Two-tailed Student’s t-test, two-way ANOVA with Bonferroni’s multiple comparisons test (Fig. 6f,l, Extended Data Fig. 10c,f), one-way ANOVA with Tukey’s multiple comparisons test (Extended Data Fig. 10h,j) were performed. *p<0.05, **p<0.01, ***p<0.001, n.s. p>0.05. The exact p value is specified in the legends. The graphs were generated using OriginPro 9.1 (OriginLab) and GraphPad Prism 7 and 8.
Sun F., Zhou J., Dai B., Qian T., Zeng J., Li X., Zhuo Y., Zhang Y., Wang Y., Qian C., Tan K., Feng J., Dong H., Lin D., Cui G, & Li Y. (2020). Next-generation GRAB sensors for monitoring dopaminergic activity in vivo. Nature methods, 17(11), 1156-1166.
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9

Statistical Analysis of Experimental Data

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Comparisons between two groups were performed using Student unpaired t test. All statistical analyses were performed with Graphpad Prism 7 and 8 (GraphPad). Error bars show SEM, as indicated in the legends, and P < 0.05 was considered statistically significant. (∗ indicates p < 0.05; ∗∗, p < 0.01; ∗∗∗, p < 0.001; ns, not significant).
Kontaki H., Koukaki M., Vasilarou M., Giakountis A., Deligianni E., Luo X., Kim Y, & Talianidis I. (2021). Targeting Smyd3 by next-generation antisense oligonucleotides suppresses liver tumor growth. iScience, 24(5), 102473.
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10

Quantitative Image Analysis of Cellular and Neural Responses

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Imaging data from cultured cells, acute brain slices, and transgenic flies were processed using ImageJ 1.52p software (NIH). The fluorescence response (ΔF/F0) was calculated using the formula (F–F0)/F0, in which F0 is the baseline fluorescence signal. The signal-to-noise ratio (SNR) was calculated as the peak response divided by the standard deviation of the baseline fluorescence fluctuation. The cross-correlation analyses were performed using NeuroExplorer 5 (Nex Technologies) and GraphPad Prism 7. Values with error bars indicate mean ± s.e.m.. The statistical analyses were performed using GraphPad Prism 7 and 8. Two-tailed Student’s t-test, two-way ANOVA with Bonferroni’s multiple comparisons test (Fig. 6f,l, Extended Data Fig. 10c,f), one-way ANOVA with Tukey’s multiple comparisons test (Extended Data Fig. 10h,j) were performed. *p<0.05, **p<0.01, ***p<0.001, n.s. p>0.05. The exact p value is specified in the legends. The graphs were generated using OriginPro 9.1 (OriginLab) and GraphPad Prism 7 and 8.
Sun F., Zhou J., Dai B., Qian T., Zeng J., Li X., Zhuo Y., Zhang Y., Wang Y., Qian C., Tan K., Feng J., Dong H., Lin D., Cui G, & Li Y. (2020). Next-generation GRAB sensors for monitoring dopaminergic activity in vivo. Nature methods, 17(11), 1156-1166.
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