Mann–Whitney test performed in GraphPad Prizm 9 was used to compare the animal weights, alpha diversity and histological measurements. Alpha diversity indicators were previously calculated using Phyloseq R package. Distance matrices (UniFrac and Bray–Curtis) were calculated from the rooted Newick OTU tree (the tree was obtained in QIIME 2), in the Microeco R package, which was also used to calculate all beta diversity, including PCoA and PERMANOVA. Metastats function for univariate analysis was performed in Microeco and plotted in GraphPad Prizm 9.
Prizm 9
Manufactured by GraphPad
Sourced in United States
Prizm 9 is a graphing and data analysis software designed for scientific and research applications. It provides tools for creating high-quality graphs, performing statistical analyses, and visualizing data. The software supports a wide range of data types and offers a user-friendly interface for efficient data management and analysis.
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Lab products found in correlation
18 protocols using prizm 9
1
Comprehensive statistical analysis of microbiome data
2
Statistical Analysis of Experimental Data
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Results were analyzed with GraphPad Prizm 9 software. All data are expressed as mean ± SEM. Difference between groups were determined using 2-way ANOVA with Tukey’s and Bonferroni’s multiple comparison test, 1-way ANOVA with Dunnett’s multiple comparison test, Mann-Witney’s or 2-tailed unpaired t-test. P<0.05 was considered to be statistically significant difference.
3
Correlation and Gene Set Analysis of Organoid-Biopsy Data
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For correlation analysis, normalized gene expression matrices were obtained across all the organoid and biopsy samples. Correlation scores (R2) were obtained by individually comparing each enteroid or colonoid sample with all the biopsy samples using linear regression model from stats package (v3.6.2). Summaries of Welch two sample t tests along with boxplots and heatmaps are provided to compare the correlation score between subject-matched enteroid/colonoid-biopsy pairs and random pairs. In GSEA, the enrichment of different gene set from KEGG database is compared between organoid and biopsy data. Fisher exact test was performed on the number of genes enriched toward disease samples vs control samples for each of the gene sets, to test if the DEGs within each gene set were from the same distribution between the organoid and biopsy data. The statistics for gene expression changes measured by qRT-PCR were calculated in GraphPad Prizm 9 software.
4
Quantitative Immune Profiling Protocol
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Shannon diversity indices were calculated using python3. All data comparisons and Spearman correlations were performed using GraphPad Prizm 9 software. The association between the presence of cluster-related TCRs and HLA alleles was calculated by the Fisher exact test using the SciPy python3 library. The donor-specific set of peptides predicted to bind to HLA class I (8-11 amino acids) and class II (15 amino acids) was calculated using NetMHCpan 4.1. Data are presented as median ± IQR; *p < 0.05, **p < 0.01, ***p < 0.001, ****p ≤ 0.0001. A p-value < 0.05 was considered statistically significant.
5
Comparative Statistical Analysis of CITE-Seq and Transposon Barcoding
6
Statistical Analysis of Experimental Data
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Statistical analysis was performed using GraphPad Prizm 9. The specific statistical tests used, details of technical replicates and summary of mean data ± standard deviation are included in the legend of each figure. In summary, instances comparing two groups utilized paired t-tests or unpaired t-tests where appropriate with P<0.05 indicating significance. Instances comparing three or more groups of data utilized One way ANOVA analysis with post hoc analysis, Tukey's multiple comparisons test was used. The P values are indicated in each figure or figure legend.
7
Statistical Analysis Techniques for Research
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All statistical analyses, including unpaired two-tailed t-test, ANOVA analysis, Spearman correlation, were performed in GraphPad Prizm 9 (San Diego, CA).
8
Statistical Analysis of Experimental Data
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All statistical analyses, including unpaired two-tailed t-test, ANOVA analysis, Spearman correlation, were performed in GraphPad Prizm 9 (San Diego, CA).
9
Statistical Analysis of Experimental Data
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Data analysis was performed in Prizm 9 (GraphPad) software. Normality tests were done using D’Agoustino and Pearson Omnibus. Data were analyzed by t-test or Mann-Whitney test for comparison of the means between two groups; one-way ANOVA with post hoc Tukey test or the Kruskal-Wallis test with Dunn’s multiple comparison test for Gaussian or non-Gaussian distributions, respectively; or two-way repeated measures ANOVA with post hoc Šídák’s multiple comparisons test for comparison of the means from different time points. Outliers were removed when they were greater than two standard deviations away from the mean. Values at p ≤ 0.05 were considered significant.
10
In Vitro and In Vivo Comparative Analysis
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A one-way ANOVA and Tukey’s post hoc test were used for the comparison of the in vitro results (SPSS ver 25.0, Chicago, IL, USA). To compare the in vivo results, the Kruskal–Wallis test was performed, followed by the Mann–Whitney U post hoc test (Prizm 9, GraphPad, San Diego, CA, USA). Statistical significance was accepted for p < 0.05 in all the statistical analyses.
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