Extended Data Figure 2. Analysis of scRNA-Seq data with Monocle, SCUBA, RaceID and PCA.

a, Pseudotemporal ordering of all 382 hematopoietic progenitors along the 9 identified Monocle cell states. These states were identified from the original four annotated flow cytometric gates, based on 5,110 Monocle identified genes (p<0.01). b, Hierarchical clustering of the 1000 most significant genes for the 9 Monocle states (correlation and ward hierarchical clustering for genes). c, SCUBA pseudotemporal ordered cell states. d, Hierarchically clustering of the 1000 most variable SCUBA genes. e, RaceID identified k-means cell clusters. f, RaceID t-SNE visualization of these cells and k-means cell states. g, Heatmap of the t-SNE based cell-state ordering and the top 150 most significant RaceID genes associated with each of the 14 k-means clusters. Gene-set predictions are assigned on the left of the heatmap following ImmGen gene-set enrichment analysis in AltAnalyze. h, Hierarchical clustering of 584 PCA identified genes using the workflow outlined by Treutlein B, et al.⁴⁷.