Epithelial cell-specific QC filtering
Epithelial cells were analyzed separately from the immune and stromal cells. A cluster of epithelial cells in patient 26 was identified as small intestinal epithelial cells from the adjacent nonmalignant tissue and excluded from further analysis. A minimum threshold of 1,742 genes per cell was set based on the local minimum in the observed bimodal distribution of genes per cell to exclude cells with low gene counts that likely represent dead cells.