Supplementary Figure 11: Monocle2 embedding of thymic hematopoietic cells observed with single-cell RNA-seq.
From: Inferring population dynamics from single-cell RNA-sequencing time series data
(a,b) Monocle2 pseudotime (a) and time (b) superimposed on monocle2 embedding based on n = 10705 cells. (c) Gene expression as function of pseudotime with spline interpolation (Nat. Methods, Qiu X. et al., 2017) of genes related to beta-selection: Rorc, Bcl2l1 (Bcl-xL) and Bcl2. (d-k) Cell counts in hexagonal cell state bins in monocle2 embedding by clusters of thymocytes (defined in Supplementary Fig. 2b) with n = 1314 cells in 0_stem (d), 1494 cells in 1_DN2a (e), n = 2930 cells in 2_Phase2 (f), n = 2018 cells in 3_Phase3 (g), n = 2103 cells in 4_DP (h), n = 117 cells in 5_NCL_ILC (i), n = 402 cells in 6_NCL_ydTC (j), n = 327 cells in 7_myeloid (k).
