The analysis of progressive HSC differentiation by scRNA-Seq. Adult Pdzk1ip1-CreER R26^tdTomato reporter mice were given a single dose of tamoxifen, and Lin⁻ Tom⁺ cells from the BM of single individual animals at the start (3 d after tamoxifen), 1, or 2 wk of tracing were isolated and profiled by scRNA-Seq. (A) Unsupervised clustering of individual cells pooled from all time points. Shown is tSNE plot (arbitrary units) of individual cells colored by the cluster (Cl.). (B) Top 10 differentially expressed genes within each cluster in A. Shown is a heat map with the level of indicated genes (rows) in individual cells (columns) expressed on a color scale representing z-score distribution. (C) Feature plots showing the expression of the indicated TFs in individual cells on the same tSNE plot as in A. Shown are factors characteristic of undifferentiated HSCs/progenitors (Mecom and Hlf); HSCs and MEPs (Tal1 and Gata2); and erythroid (Gata1 and Klf1), myeloid (Spi1), and lymphoid (Tcf7 and Ebf1) differentiation. The range of color scale of log₁₀ normalized gene counts is indicated for each feature plot. (D) The fraction of cells from each cluster among the cells at each time point. (E) Cells from the indicated time points highlighted in the same tSNE plot as in A.