Single-cell transcriptomics of mouse hair follicle

The barcoded single-cell 3′ cDNA libraries were generated using Chromium Single Cell 3′ gel bead and library Kit v3 (10x Genomics) and sequenced using an Illumina NextSeq-500. The raw data were aligned to the mouse reference genome (mm10-2020-A) using the 10X Genomics Cell Ranger pipeline (v6.0.1). The data analysis was performed in R using the Seurat package version 4.0^{72 (link),73 (link)}. Cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained. We obtained a total of 3957 and 8627 high-quality cells for telogen and anagen samples, respectively. For further analysis, all samples were merged, the transcript counts were log-normalized, and the expression of each gene was scaled so that the variance in gene expression across cells was one, followed by Principal Component Analysis (PCA). The data integration was performed by PCA embeddings using Harmony^{74 (link)}. The corrplot R function was used to measure the correlation between the two biological replicates. Differentially expressed genes (DEGs) were identified by ‘FindAllMarkers’ function using the Wilcox Rank Sum test.