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Fig. 3 | BMC Biology

Fig. 3

From: Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells

Fig. 3

Gene expression is more impaired during aging in non-primed clusters with loss of differentiation and gain of hemostasis signatures. a Heatmap of the most significant differentially expressed genes (DEGs) during aging (p value < 0.05 and log fold change > 0.5 in at least one cluster) in the different clusters revealed by Seurat analysis (Fig. 1b). The lineage-primed clusters are gathered and labeled as primed. The upper colored bars indicate cluster identity according to the color code in Fig. 1b. The lower colored bars indicate the proportion of young (orange) and aged (purple) cells in a given cluster. Gene expression are standardized across the entire dataset. b Combined violin plots showing signature scores (x-axis) in young (orange) and aged (purple) conditions per cluster. Signature scores represent the global expression of annotated genes for selected terms from enrichment analysis issued from DEGs during aging (p value < 0.05 and log fold change > 0.25 in at least one cluster) and for the HSC aging signature of Svendsen et al. (significant enrichment, hypergeometric test p value < 10−78). Significant terms (enrichment gprofiler p value < 0.05) are: Hematopoietic or Lymphoid Organ Development (HLOD) retrieved from GO:Biological Process, Hemostasis (HEM) retrieved from REACTOM pathways, Cell Adhesion Molecule (CAM) retrieved from KEGG pathways, MHC protein complex (MHC) retrieved from GO:Cellular Component, Transcriptional Miss-regulation in Cancer (TMC) retrieved from KEGG pathway. See supplementary Tables 7A & B for the lists of genes enriched in the terms. Stars show significant differences between the signature scores of young and aged cells, per cluster (average score difference > 0.1 and p value < 0.05). c Combined violin plot showing aging marker expression in young (orange) and aged (purple) conditions for the different clusters. Stars show significant differences of gene expression between young and aged cells (average log fold change > 0.25 and p value < 0.05)

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