Fig. 2: Transcriptomic profiling of etoposide-treated cells.

A Experimental timeline. B UMAP projection of scRNA-seq results with cells colored by etoposide dose (left), cell-cycle phase according to Seurat (middle), and clustered by gene expression similarity, where arrows depict two paths or bridges to senescence (right). C Proportion of each cluster in B by etoposide dose, and key with interpretation of the cell-cycle state of each cluster. D MCF10A cells were treated with 2.5 μM, 10 μM, or 25 μM etoposide for 24 h, followed by a 6 d drug-free recovery. Cells were stained for phospho-Rb (S807/811) and Hoechst for DNA content and plotted as a density scatter where yellow indicates a large number of cells in that region. The same number of cells is plotted for each dose. Red box indicates the 4 N/pRb^low cells, a hallmark of cells that have experienced a mitotic slip. Number of cells and replicates in Supplementary Data 2. E UMAP projection colored by log-normalized expression for 10 canonically used senescent markers. F UMAP projection colored by log-normalized and scaled expression for two top single-gene markers (ranked by log₂FC * (−log(p.adjusted))) from cluster 7 (quiescence-senescence transition cluster) and clusters 4, 9, 12, and 10 (senescent clusters).