scRNA-seq analysis code: Wnt/β-catenin activation in the skin NG2-expressing cell lineage

This repository contains the R Markdown workflow used for the analysis of single-cell RNA-sequencing data from the Cspg4/NG2 lineage in mouse skin following constitutive activation of Wnt/β-catenin signaling. The dataset comprises NG2-tdTomato-positive cells isolated from control and Ctnnb1^ΔEx3 mice at 7 and 14 days after tamoxifen induction.

The workflow documents quality control, doublet removal, cell-cycle scoring and regression, CCA-based dataset integration, dimensionality reduction, clustering, reference-assisted cell-type annotation using the adult mouse skin atlas of Joost et al. (2020), identification of cluster marker genes, analysis of cell-population composition and cell-cycle distribution, and visualization of selected transcriptional programs. It also includes downstream analyses used to examine TGF-β/BMP signaling, extracellular matrix remodeling, and contractility-associated gene expression.

The code accompanies the manuscript “Sustained Wnt activation remodels the epithelial–stromal niche to accommodate benign hair follicle expansion.”