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. Author manuscript; available in PMC: 2019 Mar 19.
Published in final edited form as: Cell Rep. 2018 Dec 11;25(11):2992–3005.e5. doi: 10.1016/j.celrep.2018.11.056

Figure 3. Single-cell RNA-sequencing reveals heterogeneity in the hematopoietic stem cell compartment that is altered with age.

Figure 3.

(A)-(E) LT-HSCs, ST-HSCs and MPPs from 5 young and 4 aged mice were stimulated with LPS and Pam3CSK4 and sorted for scRNA-seq. scRNA-seq data for all cells, projected on two t-SNE axes. (A) Density-based clusters. (B)-(E) Single-cell t-SNE plots (as before) indicating all cell types among (B) unstimulated and (C) stimulated cells, and mouse ages among (D) unstimulated and (E) stimulated LT-HSCs. (F) Correlation across cells between DE genes common to both simulated cluster 3 vs 2 and unstimulated aged vs young LT-HSCs. Three clusters of correlated genes are identified. (G) Heat-map represents the expression values of genes in the unstimulated myeloid-biased gene signature for each single unstimulated LT-HSC. The panels below show the myeloid signature score for each cell and is the basis for the ordering of the x axis. The bottom color-coded bar shows the age of the animals from which the cells were derived. (H) Enrichment of transcription factor motifs in enhancers of cluster 3-vs-2-specific genes for all cells (left), or only aged LT-HSCs (right) (x-axis) and differential expression of the TF genes themselves in the same comparison (y-axis). Significant genes (FDR<0.1) are indicated. An enrichment score > 0.5 indicates that the TF motif is enriched among genes that are expressed more highly in cluster 3, while a score below 0.5 indicates that the TF is expressed more highly in cluster 2.