*4.9. Statistics*

Tissue sti ffness and density were statistically analyzed with an unpaired *t*-test using software GraphPad Prism 7 (La Jolla, CA, USA). MS data were manually curated prior to statistical testing to remove single peptide hits, proteins with missing values for more than 25% per sample group for decellularized scaffolds, and proteins with 50% missing values for the repopulated samples groups.

RStudio version 1.1.442 (RStudio Team (2015). RStudio: Integrated Development for R. RStudio, Inc., Boston, MA, USA) was used for statistical analyses and for generation of heat maps, scatter plots, bar graphs, correlograms etc. Unsupervised hierarchical clustering was performed using the ward.D2 method and Euclidean distance for both row and column clusters. MS data were statistically analyzed with a Student's *t*-test and was followed by Benjamini–Hochberg correction for multiple testing of *p*-values. Statistical evaluation of single proteins was statistically analyzed with a Student's *t*-test treating each technical replicate as an individual data point.
