Transcriptome of spontaneous quiescence versus forced quiescence.
(A) Density plot of log2 fold change of transcriptomes in various forms of quiescence. For spontaneous quiescence, the fold change is calculated as the ratio of expression levels in sorted p21high versus sorted p21low cells. For other forms of quiescence, the fold change is perturbed cells versus control cells. (B) PCA analysis of all samples, for mCitrine-p21 knock-in clone 2e2. Control samples are untreated, unsorted cells. Dashed ovals indicate clusters. (C) Venn diagram of gene sets differentially regulated in five forms of quiescence. Note: the area of each set does not strictly correlate with the number of genes contained within. (D) Volcano plot (top) and distribution of log2 fold change (bottom) of p53 targets (purple) and DREAM complex targets (blue). Dash lines mark p = 0.05 threshold for gene differential regulation (top). The p-values from Mann–Whitney U test indicate significant down-regulation of DREAM targets in all forms of quiescence and significant and strong up-regulation of p53 targets in spontaneous quiescence only. Underlying data for this figure can be found in the GEO database under accession number GSE122927. DREAM, dimerization partner, RB-like, E2F4, and multi-vulval class B; GEO, Gene Expression Omnibus; PCA, principal component analysis.