Rstudio 2021

Descriptive statistics summarizing the characteristics of the included EEs, the condition of CHEERS items and the results of CHEERS scores were reported by Microsoft Excel 2020. The Kruskal–Wallis test and Mann–Whitney U test were performed to explore the potential relationship between reporting quality and various characteristics of EEs using RStudio 2021.09.0. A p-value of < 0.05 was considered as the threshold for statistical significance.

R software 4.1.2 and RStudio 2021.09.1 + 372 (Boston, USA) were used for data analysis and visualization. The comparison of gene expression between two groups was assessed by the two-tailed unpaired t-test using GraphPad Prism 9.0 (California, USA). The results were presented as means and standard deviations. Unless otherwise stated, the p value < 0.05 was considered statistically.

The statistical analyses were performed with statistical software RStudio 2021.09.1. The Shapiro–Wilk test was employed for assessing the normality of the distribution of results, while the F-test was used to analyze the equality of variances in study groups. Two-tailed Student’s T-test was used for paired comparisons of normally distributed results, while the Mann–Whitney U test was applied to analyze the data that significantly deviated from the normal distribution. P values < 0.05 were considered as statistically significant. The results of microRNA expression quantification were correlated with serum PSA levels using a linear regression analysis. The results were presented as Pearson correlation coefficients (r) and the corresponding p values. The area under the curve (AUC) was calculated through a receiver-operating characteristic (ROC) curve analysis to determine the sensitivity and specificity of the potential biomarkers. Patients with missing data on some of the prognostic parameters were excluded from the association analyses relevant for that exact parameter.

Data are expressed as mean ± SEM. P < 0.05 was considered significant. Student’s t-test (two-tailed) was used to determine differences between two groups. One-way ANOVA followed by respective post-hoc analysis (Tukey’s test) was used for statistical comparison of more than two groups. Data are displayed for at least three independent biological replicates, except for the scRNA-seq of stromal cells from assembloids and epithelial cells from assembloids, organoids, and colon tissue, for which two biological replicates per group were used. In Figs. 1b–e, h; 2a, b, f; 3d, e; 4a, h; Supplementary Figs. 1a, c-h; 2c, d; 4a–c; 5a; 8a, b, e–g, at least three independent experiments were performed with similar results. In Figs. 1g, 3g, 4c; Supplementary Fig. 2a, b, the average percentage of specific epithelial cells from three biological replicates was analyzed. In Figs. 3c, h, 4d–f; Supplementary Fig. 7a, e, signal areas in random fields of view from three biological replicates were analyzed. In Supplementary Fig. 8c, d, all organoids in three Matrigel drops each group from three biological replicates were analyzed. GraphPad Prism 8, R 4.2.2, and RStudio 2021.09.1 were used for data visualization and statistical analysis.