Supplementary Figure 1: Overview of all thymic hematopoietic cells (n = 10,895) observed with single-cell RNA-seq.
From: Inferring population dynamics from single-cell RNA-sequencing time series data
(a-f) Time (a-c) or louvain group (d-f) label superimposed on cells in t-SNE based on data processed for louvain clustering (a,d), in in t-SNE based on data processed for diffusion pseudotime analysis used throughout the paper (b,e) and in diffusion map based on data before filtering of putative myeloid or dendritic cells (c,f). See also Supplementary data 1.2 for the further details on this analysis. (g) Cell type labels for louvain groups from marker genes. stem: hematopoietic stem cells, DN2a/b (double-negative T-cells), phase 2 (Nat. Rev. Immunol. 14, Yui, M. A. & Rothenberg, E. V., 2014), phase 3 (Nat. Rev. Immunol. 14, Yui, M. A. & Rothenberg, E. V., 2014) and DP (double-positive T-cells) are T-cell maturation stages, NCL_ILC: non-conventional lymphoid cells (Immunity, Kernfeld, E. M. et al., 2018) with innate lymphoid cell character, NCL_ydTC: non-conventional lymphoid cells with γδ-T-cell cell character, myeloid: putative myeloid and dendritic cells. (h) T-cell development phase across merged louvain groups from (g). (i) Abstracted graph from paga (bioRxiv, Wolf F. A. et al., 2017) at a connectivity threshold of 0.02 with cluster identity superimposed. See also Supplementary data 1.2 for the further details on this analysis.
