Statistical analysis was performed using Prism 9 for MacOS (v9.4.0, GraphPad Software LLC., San Diego, CA, USA). Categorical demographic and clinical features distributions were analyzed through two-tailed Chi-square test. Continuous outcomes were confirmed normally distributed through Shapiro-Wilk test and analyzed using two-tailed unpaired t-test. If not parametric, a two-tailed Mann-Whitney test was employed. Finally, temporal data was assessed through Two-Way ANOVA with Geisser-Greenhouse correction, followed by post-hoc Tukey’s test (>2 categories) for multiple comparison or Sisak’s multiple comparison test (2 categories). Data is presented as means ± standard deviation. The significance level was set at p < 0.05. Graph plots were created by Prism 9 for MacOS (v9.4.0, GraphPad Software LLC., San Diego, CA, USA) and illustrated using Adobe Illustrator (v26.3.1, Adobe, San Jose, CA, USA).
Prism 9 for macos
Manufactured by GraphPad
Sourced in United States, Belgium
Prism 9 for macOS is a software application developed by GraphPad for data analysis, graphing, and visualization. It provides a range of tools and features for scientists and researchers to manage, analyze, and present their data.
Automatically generated - may contain errors
Lab products found in correlation
Stata 16, by StataCorp (3 mentions)
Spss statistics version 26, by IBM (2 mentions)
Odyssey clx, by LI COR (1 mentions)
Celltag 700 stain, by LI COR (1 mentions)
Irdye 800cw, by LI COR (1 mentions)
Bio glo luciferase assay system, by Promega (1 mentions)
Spss statistics 21 for windows, by IBM (1 mentions)
Nis elements advanced research software, by Nikon (1 mentions)
Stata version 13, by StataCorp (1 mentions)
Dmi600b, by Leica (1 mentions)
Quantstudio 3, by Thermo Fisher Scientific (1 mentions)
Sybr green pcr master mix, by Thermo Fisher Scientific (1 mentions)
Amv reverse transcription system, by Promega (1 mentions)
Quick rna miniprep plus kit, by Zymo Research (1 mentions)
Spss statistics software, by IBM (1 mentions)
Spss statistics 25, by IBM (1 mentions)
Spss for mac version 26, by IBM (1 mentions)
Illustrator 23, by Adobe (1 mentions)
Spss for macos, by IBM (1 mentions)
R version 4, by R Project for Statistical Computing (1 mentions)
91 protocols using prism 9 for macos
1
Statistical Analysis of Biological Data
2
Quantitative Analysis of Virus Infection
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RV-infected MA104 cells (1 × 104) were seeded in a 96-well black tissue culture plate (Greiner). At indicated times postinfection, cells were fixed with 2% paraformaldehyde in PBS for 10 min at room temperature, followed by permeabilization with 0.1% Triton X-100-PBS for 10 min at room temperature. Next, cells were blocked with 2% BSA in PBS for 1 h at room temperature and then incubated with primary antibodies diluted in blocking buffer for 1 h at room temperature in the shaker. Then, the cells were incubated with the corresponding secondary antibody conjugated to IRDye 800 CW (LI-COR). The cell signal was normalized using CellTag 700 stain (LI-COR) diluted at 1:800. The cells were washed three times with 0.01% Tween 20 in PBS between incubations. Samples were acquired using an Odyssey CLx (LI-COR) followed by data analysis and normalization in Microsoft Excel for Mac version 16.58. Statistical analysis, unpaired Student's t test, and plots were performed using Prism 9 for macOS version 9.3.1 (GraphPad Software, LLC).
3
Statistical Analysis of Cognitive Studies
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Data analyses. Sample sizes were determined by power analysis using G*Power (v.3.1.9.2) based on previous works published by our lab on CBF regulation cognitive testing [25 (link), 33 (link)]. The experiments were randomized based on the random number generator (https://www.random.org ) and were performed and analyzed in a blinded fashion whenever possible. Data and image analyses were done using ImageJ 1.54c (NIH) or Prism 9 for MacOS (GraphPad Software). Data were tested for normal distribution by the D’Agostino–Person test and for outliers by the Grubbs’ test (extreme studentized deviate). Two-group comparisons were analyzed using paired or unpaired two-tailed t-test, as indicated. Multiple comparisons were evaluated by one-way or two-way analysis of variance (ANOVA) and Tukey’s test. Differences were considered statistically significant for probability values less than 0.05. Data are expressed as the mean ± S.E.M.
4
Biomarker Correlation with Illness Severity
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Continuous data (e.g., dog characteristics, physical examination findings and clinicopathologic values) were assessed for normality using the D’Agostino Pearson test and appropriate descriptive statistics calculated. Correlations between C18 and HILIC prognostic biomarker abundance and illness severity scores (APPLEfast) were calculated using non-parametric methods (Spearman’s r) following natural log transformation of the abundance data. General statistical analyses were performed using commercial software (Prism 9 for macOS, GraphPad, La Jolla, CA) with alpha set at 0.05.
5
Pseudotyped Lentivirus Production and Neutralization Assay
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Single-round pseudotyped lentivirus particles were produced by the cotransfection of HEK293T cells with the pHAGE-CMV-Luc2-IRES-ZsGreen-W (Cat# NR-52516, BEI), HDM-Hgpm2 (Cat# NR-52517, BEI), HDM-tat1b (Cat# NR-52518, BEI), pRC-CMV-Rev1b (Cat# NR-52519, BEI) and a SARS-CoV-2 spike plasmid as previously described48 (link). Virus-containing supernatants were harvested 72 h post-transfection, filtered using 0.45 μm syringe filters, aliquoted and stored at −80°C until further use. For neutralization assays, the virus was diluted to yield ~ 50,000 relative light units (RLU)/well and incubated for 1 h at 37°C with 2-fold dilutions of heat-inactivated serum. Cells were then infected in quadruplicate and lysed 72 h later using the Bio-Glo luciferase assay system (Cat# GT7940, Promega, Madison, WI, USA) to measure luciferase activity. The percentage of neutralization was calculated based on the RLU measured using the virus-only control. The half-maximal effective concentration (EC50) titers were calculated using a log (agonist) versus normalized response (variable slope) nonlinear function in Prism 9 for macOS (GraphPad).
Alternatively, IMMUNO-CRON and IMUNO-COV v2.0 (Imanis Life Sciences)138 (link), which use a luciferase-encoding VSV displaying SARS-CoV-2 spike glycoproteins, were used to measure pseudovirus nAbs.
Alternatively, IMMUNO-CRON and IMUNO-COV v2.0 (Imanis Life Sciences)138 (link), which use a luciferase-encoding VSV displaying SARS-CoV-2 spike glycoproteins, were used to measure pseudovirus nAbs.
6
Analyzing Effector Cell Cytotoxicity
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Statistical analyses were conducted using Prism 9 for macOS (GraphPad). The log-rank test was used for survival analyses between the two indicated groups. A two-way ANOVA was employed to assess the significance of differences among the various effector cells (NK cell, m-reMAIT cells, and NK cells plus m-reMAIT cells) in lysis assays.
7
Survival Analysis using Prism 9
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Survival curves and analysis were done using Prism 9 for macOS (GraphPad Software, San Diego, CA). The significance p values were determined using the Mantel-Cox log rank test.
8
Quantifying Inflammatory Cytokine Levels in cGAMP-Treated Cells
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Concentrations of CCL5 and CXCL10 as determined by ELISA were log transformed prior to comparison between control and cGAMP-treated cells using multiple paired t-tests. Samples measuring below the lower limit of detection (LLD) were set to a value of 0.5*LLD. RT-qPCR data were analyzed by log2 transforming fold change (2-ΔΔCt). A one-way ANOVA and Dunnett’s or Tukey’s multiple comparisons test were used to compare expression between cell lines, and timepoints post RT to NIR controls. Multiple t-tests were used to compared cGAMP-treated cells to control cells. A two-way ANOVA and Dunnett’s multiple comparisons test was used compare gene expression post radiation between control and STING-KD cell lines. Statistical analysis was performed using Prism 9 for MacOS, v9.4.0 (GraphPad Software). P values less than 0.05 were considered statistically significant. P values for all comparisons made are listed in S2 Table .
9
Multiparametric MRI Characterization of IDH Mutation
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Statistical analysis was performed using Prism 9 for macOS (GraphPad Software, San Diego, CA, USA). The relationship between mrT1/T2 and IDH mutation status was investigated by Mann–Whitney U test and receiver-operating characteristic (ROC) curve analysis. A p-value of less than 0.05 was considered significant. t-Distributed Stochastic Neighbor Embedding (t-SNE) analysis was used to investigate the difference in MRI qualities and characteristics among the three cohorts. Rtsne package version 0.15 for R with default parameters was used for this analysis (Tables S3 , S4 , and S5 )26 .
10
Statistical Analysis of Experimental Data
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The Shapiro-Wilk W test was used to test the normality of data. Parametric 2-group comparisons were conducted by the unpaired t-test. Non-parametric 2-group comparisons were conducted by the Mann-Whitney U test. The chi-square test was used for comparison by sex. Three-group comparisons were conducted using one-way analysis of variance (ANOVA). In addition, if there were significant differences, Tukey’s multiple comparisons test or Dunnett’s multiple comparisons test was used for subsequent testing, as a post hoc test, as needed. Relationships between variables were assessed using Spearman’s rank correlation coefficients. p < 0.05 was considered statistically significant. Statistical analyses were conducted using SPSS Statistics 21 for windows (IBM Corporation) and Prism 9 for macOS (GraphPad Software).
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