Figure 2

Identification of cell types in HCC samples. (A) The violin plots of total gene counts (nCount), number of gene types (nFeature) and the percentage of reads that mitochondrial genes (percent.mt) in each sample of HCC patients from GSE149614. (B) A subset of features that shows high variation between cells. Red dot: top 2000 genes that vary significantly in expression between cells, the top 10 highly variable genes were labeled. Black points: Genes with consistent expression level between cells. (C) Marker genes extracted from each cell types displayed in 15 Principal Component. (D) tSNE plots of 16 liver cancer patients sample between primary tumor (T) and adjacent non-tumor liver (N). Each color marks a cell of one patient to visualize 16 cell classes. (E) tSNE that showed the distribution of typical marker (hepatocyte and HCC cell-ALB, endothelial cell-CD34, stem cell-EPCAM, stromal cell-NGFR, B cell-MS4A1, T cell-GNLY, CD3E and CD8A, NK cell-KLRD1, monocyte-CD14 and FCGR3A, macrophage-CD68) representing one cell type in all cells. (F) tSNE plots of 9 cell types. (G) tSNE plots of hepatocytes and HCC cells. (H) Total gene counts (nCount), number of gene types (nFeature) and percentage of mitochondrial genes (percent.mt). Each dot represents a hepatocyte or HCC cell. (I) Total gene counts (nCount), number of gene types (nFeature) and percentage of mitochondrial genes (percent.mt). Each dot represents a hepatocyte or HCC cell (grouped by sample).