Single-cell RNA and TCR sequencing analysis.
All downstream analyses were performed using Cell Ranger 7.0 and the R package Seurat (v4.0.4). Outlier gene detection rates (nFeautre_RNA <300 and >14,000) and high mitochondrial transcript load (>10%) were filtered from the analysis. The data were normalized using Seurat’s logNormalize with a scale factor of 10,000. Data from individual samples were combined into a single expression matrix after scaling. Then, the cell cycle scores were set as variables to regress out. The Uniform Manifold Approximation and Projection (UMAP) algorithm was used to reduce and visualize dimensionality, followed by the construction of a clustering analysis. DEGs among clusters were detected by the Seurat function “FindAllMarkers.” Select functional DEGs in each cluster were visualized via stacked violin plots. Volcano plots of DEGs (