Abstract <p>The mouse digit tip regeneration model is one of the most phylogenetically close models to the human, and studying it at the cellular and transcriptomic levels may allow the development of novel approaches in regenerative medicine. Two papers with single-cell RNA sequencing applied to this model have been published, but none of them aimed to analyze differential gene expression between blastema and uninjured cells. In our study, we aim to conduct this analysis. All data processing stages, including cell filtering, clusterization, integration, and differential gene expression analysis were carried out in R with the aid of the Seurat package. Based on the presence of intermediate phenotypes after clusterization, we found out that epithelial-mesenchymal and endothelial-mesenchymal transitions may occur during digit tip regeneration, but not in uninjured samples. Differential gene expression analysis yielded about 1000 genes between stromal cells in blastema and uninjured digits in both analyzed datasets. These genes were associated both with morphogenetic processes: ossification, angiogenesis, extracellular matrix organization, and cell adhesion, and with a number of metabolic processes. We also selected from this differentially expressed gene set transcription and paracrine factors, among which putative regulators of the described processes were found. Further research on the presented here transcription and paracrine factors may elucidate the mechanisms of digit tip regeneration.</p>