Figure 2

Validation of the CCS method using datasets of the HCT116 cell cycle and quiescence-induced cells. (A) CCS score heat maps for the HCT116 cell cycle dataset. Synchronized HCT116 cells were profiled at 0, 2, 4, 6, 7, 8, 9 and 10 h after release (DMSO, 0–10 h). Nocodazole-treated cells were profiled in parallel (Ncz, 7–10 h). CCS scores were calculated for both the total (upper panel) and the cycling (lower panel) gene dataset. Each column represents an experimental sample and each row a CCS subset. Cell cycle phases for CCS are indicated by the colored bars on the left of each map (G1; cyan, S; purple, G2; yellow, and M; red). Red bars above the columns indicate estimated M phase. (B) Flow cytometric analysis of HCT116 cells. Synchronized HCT116 cells were monitored by DNA flow cytometry after release with DMSO (upper panel) or nocodazole (lower panel). (C) CCS score heat maps for the Fournier et al. dataset of HMECs grown in 3D culture. In this system, rapidly growing HMECs (day 3) enter the quiescent state over several days (day 7). (D) CCS score heat maps for the Cam et al. dataset of T98 breast cancer cells. The profiles of growing and serum-starved cells for 3 days were analyzed.