Fig. 7: A senescent gene set, EIS Boulder, to identify diverse senescent cell types following etoposide.

A Left: Distribution of module scores for cells from each cluster based on our senescent gene set, dubbed Etoposide Induced Senescence (EIS) Boulder (Supplementary Data 3). Right: UMAP with cells colored by module score for EIS Boulder. B Average scaled expression of all genes in EIS Boulder by cluster. C Left: UMAP of scRNA-sequencing data of WI38 fibroblasts cultured until replicative senescence (population doubling level (PDL) > 50, RS), exposed to 10 Gray (Gy) ionizing radiation and grown for an additional 10 d (IR), or treated with 50 μM etoposide for 7 d (ETO7d) from Wechter et al. UMAPs colored by condition or Seurat cell-cycle phase annotation. Right: UMAP colored by log-normalized expression of CDKN1A (p21) or module score for EIS Boulder. D Left: UMAP of scRNA-sequencing data of WI38 fibroblasts cultured to various PDLs from Chan et al. UMAPs colored by condition or Seurat cell-cycle phase annotation. Right: UMAP colored by log-normalized expression of CDKN1A (p21) or module score for EIS Boulder. E Distributions of expression scores of the EIS Boulder gene set for the data sets in C and D with only Seurat-labeled G1 cells plotted. F Single-cell expression scatter plots of the EIS Boulder gene set vs log-normalized CDKN1A expression for the data sets in C and D. Dots colored by condition and Loess fit in blue. Gray shading represents a 95% confidence interval. Only Seurat-labeled G1 cells plotted.