Analysis of changes in cell phenotype profiles, including Golgi morphology, during late G2 and G0/G1 transition. (A) Schematic illustrating the morphological dynamics of the Golgi and cilia throughout the cell cycle. This figure primarily focuses on Golgi dynamics in late G2, while subsequent figures address the G0/G1 transition. (B–D) Morphological feature analysis of HeLa cells in late G2. (B) UMAP plots of cell phenotype profiles in late G2. All experimental conditions are shown in a composite color scheme, with each condition also highlighted individually in Fig. S2 D. Representative images are shown in Fig. S2 B, and the features used in this analysis are detailed in Fig. S2 C. (C) Analysis of Golgi-based subclusters in the control and SP-treated groups. Data were extracted from the dist_nuc_Golgi violin plot in Fig. S2 E and divided into subclusters 1 and 2 using the SP group’s median (indicated by the magenta line in the leftmost violin plot). Distributions of three representative features, i.e., peaks_num_Golgi, peaks_xy_std_Golgi, and objects_num_golgi (number of Golgi fragments detected after skeletonization), are shown for each experimental condition and subcluster. (D) Schematic representation of typical Golgi morphologies for each subcluster, based on the analysis. (E–H) ARPE-19 cells were serum starved to arrest in G0 and induce ciliogenesis. Morphological changes were then analyzed after serum re-addition. (E) Time course of serum starvation and serum re-addition. DMSO (control) or SP was added 2 h before serum re-addition, and cells were then cultured with serum and the indicated drugs for the specified durations before fixation. For the 0-h time point, cells were fixed immediately without serum re-addition. (F) Cropped images of representative cells at 0 and 18 h after serum re-addition. Arrows indicate cilia. AcTub, acetylated tubulin. Scale bar, 20 µm. (G) Percentage of ciliated cells at each time point after serum re-addition. Numbers in the bar graphs represent absolute cell counts for each category. Cilia were detected by skeletonizing the acetylated tubulin signal. (H) UMAP visualization using features detailed in Fig. S3 B. Time points for the DMSO (control) and SP-treated groups are highlighted for clarity. DBSCAN clustering results and the proportion of cells in each cluster are also shown in the box.
Figure 2.

Analysis of changes in cell phenotype profiles, including Golgi morphology, during late G2 and G0/G1 transition. (A) Schematic illustrating the morphological dynamics of the Golgi and cilia throughout the cell cycle. This figure primarily focuses on Golgi dynamics in late G2, while subsequent figures address the G0/G1 transition. (B–D) Morphological feature analysis of HeLa cells in late G2. (B) UMAP plots of cell phenotype profiles in late G2. All experimental conditions are shown in a composite color scheme, with each condition also highlighted individually in Fig. S2 D. Representative images are shown in Fig. S2 B, and the features used in this analysis are detailed in Fig. S2 C. (C) Analysis of Golgi-based subclusters in the control and SP-treated groups. Data were extracted from the dist_nuc_Golgi violin plot in Fig. S2 E and divided into subclusters 1 and 2 using the SP group’s median (indicated by the magenta line in the leftmost violin plot). Distributions of three representative features, i.e., peaks_num_Golgi, peaks_xy_std_Golgi, and objects_num_golgi (number of Golgi fragments detected after skeletonization), are shown for each experimental condition and subcluster. (D) Schematic representation of typical Golgi morphologies for each subcluster, based on the analysis. (E–H) ARPE-19 cells were serum starved to arrest in G0 and induce ciliogenesis. Morphological changes were then analyzed after serum re-addition. (E) Time course of serum starvation and serum re-addition. DMSO (control) or SP was added 2 h before serum re-addition, and cells were then cultured with serum and the indicated drugs for the specified durations before fixation. For the 0-h time point, cells were fixed immediately without serum re-addition. (F) Cropped images of representative cells at 0 and 18 h after serum re-addition. Arrows indicate cilia. AcTub, acetylated tubulin. Scale bar, 20 µm. (G) Percentage of ciliated cells at each time point after serum re-addition. Numbers in the bar graphs represent absolute cell counts for each category. Cilia were detected by skeletonizing the acetylated tubulin signal. (H) UMAP visualization using features detailed in Fig. S3 B. Time points for the DMSO (control) and SP-treated groups are highlighted for clarity. DBSCAN clustering results and the proportion of cells in each cluster are also shown in the box.

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