Fig. 3

t-SNE analysis on imputed single-cell RNA-seq reveals more clearly subpopulations of CML stem cells. All types of these stem cells are of CP-CML in black (n = 477), normal HSCs in blue (n = 232), pre-BC samples taken from the patients presented in CP (pre-BC), 12 months and 3 months before transformation to myeloid and lymphoid BC in green (n = 185), BC-CML in purple (n = 155) and K562 in red (n = 53). Red ovals focus on the group of BC-CML stem cells. a The t-SNE analysis on the CML stem cell data without missing the imputation. b The t-SNE analysis on the CML stem cell data using the mean-smooth method with neighbor cells on the trajectory. c The t-SNE analysis on CML stem cell data using the MISC method