(a) t-SNE map of the clusters identified by RaceID3 analysis on the murine hematopoietic transcriptome data from Olsson et al.1. The cell types described in the original study were recovered and are indicated next to the clusters. (b) t-SNE maps highlighting normalized expression of lineage-specific markers. (c) FateID fate bias predictions for all lineages. (d) Scatterplot for the comparison of fate bias towards the monocyte and the neutrophil lineage. Aggregated marker gene expression is highlighted for monocytes (left; Irf8, Csf1r, Ly86), for neutrophils (middle; Gfi1, Cebpe, S100a8) and the bi-potential progenitor (right; Ctsg, Elane, Mpo). The markers are taken from Figure 1c of Olsson et al.1. The FateID analysis reveals that lineage-specific marker gene expression coincides with uni-lineage bias, while progenitors with similar fate biases for monocytes and neutrophils express markers, which are expressed in both of the lineages as well as low levels of the lineage-specific markers. This is consistent with the interpretation of Olsson et al., that these cells represent bi-potent progenitors. We note that the bi-potency of this transitional state was validated by in vitro differentiation assays in the original study. All panels show data of 382 cells sequenced from n = 3 mice.
1. Olsson, A. et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature 537, 698–702 (2016).