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Fig. 4 | Genome Medicine

Fig. 4

From: Development of double-positive thymocytes at single-cell resolution

Fig. 4

Unique division mechanism of DPbla thymocytes. a Top: Mean expression of cell cycle-associated genes (black) and all genes (gray) in each cell. Bottom: Heat map of cell cycle-associated gene expression in each cell. Genes (rows) were sorted by unsupervised clustering. Cells were ordered from DN to SP. b Single cells were assigned to different stages of the cell cycle (G1/S, S, G2/M, M, and M/G1) according to their expression of cell cycle stage-specific genes (see “Methods”). The percentage of cells located in each cell cycle stage is shown in pie charts for ISPs and DPblas (DPbla1, DPbla2, DPbla3 and DPbla4). c Expression of representative cell cycle genes in corresponding cell cycle stages. d Pearson correlation between the cell orders predicted by PBA before and after the removal of cell cycle-related genes. e The overlap ratio of the four DPbla subpopulations before and after the removal of cell cycle-related genes (see “Methods”). f, g Cell cycle stages of single cells were assigned as in Fig. 4a and are shown on a strip plot. Each dot represents one cell. Cells were ordered by PBA prediction. f Thymocytes were ordered from DN to SP for our data, Tabula Muris data and human thymus data. g Cells were ordered from early T cell progenitor (ETP) cells to DN3 cells for DN thymocytes, from multipotent progenitor (MPP) cells to erythroid cells for erythroid data and from progenitors to neurons for neuron development data. The color scheme indicates that the cell cycle periods were the same as in Fig. 4b, and gray indicates that the cell was not in the cell cycle. h The indicated cells (total thymocytes, DPblas and DPres) were sorted and stained with UltraGreen and then cultured in vitro for 24 h. Decayed fluorescence peaks represent dividing cells. The ratio of cells that divided once and twice was calculated as shown

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