Supplementary Figure 12: Predicting the fate bias of human hematopoietic progenitors with FateID.

For this analysis, single cell RNA-seq data generated by Smart-seq2 for individual 1 from Velten et al.¹ were used. (a) t-SNE map showing clusters of cells with similar transcriptomes derived by RaceID3. (b) Heatmap of log₂-transformed averaged normalized expression of known marker genes across clusters. The cluster number and color are indicated on the right. Only clusters with >3 cells were included. A hierarchical clustering dendogram is shown on the right margin. (c) Correlation of predicted fate bias and cell surface marker expression measured by index-sorting for FateID (left) and STEMNET (right). Surface expression of CD135 (encoded by FLT3) and CD45RA discriminates progenitors of neutrophils, monocytes, pDCs, and lymphocytes, on the one hand, and eosinophils/basophils/mast cells, erythrocytes and megakaryocytes, on the other hand. Surface expression of the two markers is positively correlated to fate bias towards the former group of lineages and inversely correlated to fate bias towards the latter group of lineages. FateID predictions show a more pronounced difference between the two groups. (d) Shown are t-SNE maps highlighting log-transformed fluorescence intensity measured by flow cytometry (index-sorting) for CD135 (top) and CD35RA (bottom). (e) The fate bias predicted by FateID, corresponding to the probability of a cell to be assigned to a given lineage, is color-coded in the t-SNE map. The fate bias is shown for the B cell lineage (left) and the pDC lineage (right). The black circle marks a population of cells with enhanced fate bias towards pDCs or B cells (f) Shown are t-SNE maps highlighting log-transformed normalized transcript expression of the B cell lineage marker VPREB1 (left) and the pDC lineage marker IRF8 (right). The expression domains of these markers overlap with the predicted domain of fate bias towards the respective lineage and lymphoid progenitors with enhanced bias towards the pDC lineage exhibit co-expression of the two markers (black circle). (g) The fate bias predicted by STEMNET shown for the B cell lineage (left) and the pDC lineage (right). Black circle: see (f). (h) Scatterplots comparing fate bias predicted by FateID and STEMNET for the pDC lineage (left) and the B cell lineage (right). Although the predictions are overall correlated (Spearman’s correlation coefficient is 0.74 for the B cell lineage and 0.67 for the pDC lineage), STEMNET predicts more uniform level across a larger fraction of progenitors. All panels show data from 1,035 cells sequenced from n = 1 donor.

1. Velten, L. et al. Human haematopoietic stem cell lineage commitment is a continuous process. Nat. Cell Biol. 19, 271–281 (2017).