TooManyCells identifies and visualizes relationships of single-cell clades

Purpose: To characterize heterogeneity of GSI-responsive and -resistant T-ALL cells Method: We generated GSI-resistant T-ALL DND41 cells and profiled their transcriptome using single-cell RNA sequencing. Result: We report here the presence of resistant-like subpopulation in drug naïve DND41 T-ALL cells. Conclusion: While other popular scRNA-seq clustering algorithms failed, TooManyCells, a suite of clustering and visualization algorithm developed in our lab, could identify rare resistant-like DND41 T-ALL cells. Overall design: Single-cell RNA sequencing was performed on cells acquiring resistance to a gamma secretase inhibitor (GSI) after long-term ascending-dose or sustained high-dose treatments of Notch-mutated T-cell acute lymphoblastic leukemia (T-ALL) DND41 cells.