Seurat analysis
For basic data visualization, a log-transformed gene matrix was imported
into R Studio and analyzed by the Seurat package
(http://www.satijalab.org/seurat). Cells with fewer than 500 detected
genes and greater than 10% mitochondrial gene expression were removed.
Moreover, we eliminated genes detected (UMI count >0) in
less than three cells and deleted mitochondrial and ribosomal genes. The
remaining genes were reduced in dimension by principle component
analysis. After quality control and normalization, we used T-distributed
Stochastic Neighbor Embedding (t-SNE) to visualize the characteristics
of the continuity of subsets. Using other functions of Seurat, including
FindVariableFeatures, FindAllMarkers, and Doheatmap, every cluster of
collected cells was user-redefined for further analysis.