Data from: Mitotic Cdc42 waves encode PI(3,4)P2 signaling and Golgi morphological state to control spindle scaling
Data files
May 20, 2026 version files 717.44 MB
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alpha_tubulin_radial_density_profile.ipynb
353.65 KB
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Figure_1B.xlsx
9.28 KB
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Figure_1C.xlsx
28.81 KB
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Figure_1D.xlsx
16.22 KB
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Figure_1E.xlsx
10.91 KB
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Figure_1FGHI.xlsx
15.76 KB
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Figure_2B_S2.xlsx
26.32 KB
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Figure_2CD.xlsx
251.76 KB
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Figure_2EF-KD_.xlsx
110.20 KB
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Figure_2EF-WT.xlsx
125.43 KB
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Figure_3C.xlsx
10.30 KB
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Figure_3E.xlsx
13.44 KB
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Figure_3F.xlsx
9.48 KB
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Figure_3G.xlsx
9.48 KB
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Figure_3H.hdf
196.12 MB
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Figure_3I.hdf
254.21 MB
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Figure_4AB.xlsx
26.20 KB
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Figure_4C_wave_H2B_cluster.xlsx
126.52 KB
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Figure_4DEFG.xlsx
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Figure_6C.xlsx
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Figure_6D.xlsx
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Figure_6E.xlsx
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Figure_6F.xlsx
10.90 KB
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Figure_S4A_middle_cell.hdf
197.03 MB
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Figure_S4B.hdf
68.62 MB
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mov_hue_raw.m
3.91 KB
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OS_plot_1c_peak_valley.m
6.15 KB
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panoraa_projection.ipynb
213.58 KB
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README.md
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Jun 02, 2026 version files 717.44 MB
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alpha_tubulin_radial_density_profile.ipynb
353.65 KB
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Figure_1B.xlsx
9.28 KB
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Figure_1C.xlsx
28.81 KB
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Figure_1D.xlsx
16.22 KB
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Figure_1E.xlsx
10.91 KB
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Figure_1FGHI.xlsx
15.76 KB
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Figure_2B_S2.xlsx
26.32 KB
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Figure_2CD.xlsx
251.76 KB
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Figure_2EF-KD_.xlsx
110.20 KB
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Figure_2EF-WT.xlsx
125.43 KB
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Figure_3C.xlsx
10.30 KB
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Figure_3E.xlsx
13.21 KB
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Figure_3F.xlsx
9.48 KB
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Figure_3G.xlsx
9.48 KB
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Figure_3H.hdf
196.12 MB
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Figure_3I.hdf
254.21 MB
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Figure_4AB.xlsx
26.20 KB
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Figure_4C_wave_H2B_cluster.xlsx
126.52 KB
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Figure_4DEFG.xlsx
11.04 KB
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Figure_6C.xlsx
20.55 KB
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Figure_6D.xlsx
19.60 KB
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Figure_6E.xlsx
23.91 KB
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Figure_6F.xlsx
10.90 KB
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Figure_S4A_middle_cell.hdf
197.03 MB
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Figure_S4B.hdf
68.62 MB
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mov_hue_raw.m
3.91 KB
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OS_plot_1c_peak_valley.m
6.15 KB
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panoraa_projection.ipynb
213.58 KB
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README.md
7.24 KB
Abstract
Self-organizing waves are observed in numerous biological systems and may encode spatial and temporal information for cellular organization in the absence of pre-patterns. In mitotic mast cells, periodic cortical waves emerge prior to spindle assembly with wave periods that are proportional to cell size. Here, we investigate the mechanisms that govern cortical wave scaling and examine the consequences of wave perturbation on mitotic spindle size scaling. We find that the periods of mitotic waves are regulated by the turnover of phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) on the plasma membrane, which depends on inositol polyphosphate-4-phosphatase type II (INPP4B). Genetic depletion of INPP4B increases cortical wave period and spindle length. Intriguingly, mitotic wave period could be tuned continuously during mitosis, indicating the existence of a fast, post-translational regulatory mechanism for wave scaling. We further find that the regulation of mitotic waves on the plasma membrane is controlled by the sequestering of INPP4B and PI(3,4)P2 upon mitotic Golgi fragmentation. Based on these findings, we propose a cell size-sensing mechanism in which cortical waves act like sonar waves, adjusting their timing and propagation based on the shuttling of signalling proteins between the cell cortex and intracellular organelles. This rapid communication scheme allows the cell to adjust spindle scaling dynamically, ensuring accurate cell division.
Dataset DOI: 10.5061/dryad.cfxpnvxn7
Description of the data and file structure
For scatterplots and population analysis, Excel sheets include data points used in each analysis. Each column is labelled according to the data analyzed.
For intensity plots, excel sheets include the tabs labelled with the channels analyzed, time interval, info, probe names to the respective channels.
Files and variables
File: mov_hue_raw.m
Description: This function converts a time-lapse image stack into RGB images where color encodes time (blue = earlier, red = later) to visualize motion/propagation across frames and saves the resulting “temporal hue shift” images to a folder.
File: Figure_1B.xlsx
Description: Comparison of wave periods in G2 and Metaphase
Variables
- G2 phase (seconds)
- M phase (seconds)
File: Figure_1C.xlsx
Description: Intensity plot of wave period in a dividing cell
Variables
- Channel 1: Intensity
- Time interval (seconds)
File: Figure_1D.xlsx
Description: Fourier Transformation of wave period in small vs big cell
Variables
- Channel 1: Intensity (1st column: Small, 2nd column: Big)
- Time interval (seconds)
File: Figure_1FGHI.xlsx
Description: Changes in mitotic wave periods before and after RO3363 treatment
Variables
- Channel 1: Intensity (1st column: Fig F & G, 2nd column: Fig H& I)
- Time interval (seconds)
File: Figure_2B_S2.xlsx
Description: Intensity profile of FBP17 vs Tks4
Variables
- Channel 1: FBP17 Intensity (1st column: Fig 2B, 2nd column: Fig S2)
- Channel 2: TKs4 Intensity (1st column: Fig 2B, 2nd column: Fig S2)
- Time interval (seconds)
File: OS_plot_1c_peak_valley.m
Description: To generate scatterplot in Figure 2B and C. This function smooths a single ROI intensity time series, detects peaks and valleys, computes rise/decay and inter-peak timing metrics, and saves both annotated plots and an Excel file of quantified peak–valley dynamics.
File: Figure_3E.xlsx
Description: Comparison of spindle length in WT vs INPP4B KD cells
Variables
- WT: Spindle length in WT (um)
- INPP4B KD: Spindle length in INPP4B KD (um)
File: Figure_3F.xlsx
Description: Comparison of spindle volume in WT vs INPP4B KD cells
Variables
- Spindle volume: (1st column-WT, 2nd column-INPP4B KD) (um3)
File: Figure_4AB.xlsx
Description: Wavelet analysis of cells with unchanged wave periods vs changing wave periods
Variables
- Channel 1: Intensity (1st column: unchanged, 2nd column: changed)
- Time interval (seconds)
File: Figure_2EF-KD_.xlsx
Description: FBP17 and Tks4 Wave periods in INPP4B KD cells
Variables
- Channel 1: Intensity
- Time interval (seconds)
File: Figure_2CD.xlsx
Description: Comparison of the rise and drop phases of FBP17 vs Tks4 waves
Variables
- Channel 1: Intensity of FBP17
- Channel 2: Intensity of Tks4
- Time interval (seconds)
File: panoraa_projection.ipynb
Description: For Radial Panorama View of Spindle in Figure_3H.hdf, Figure_3I.hdf, Figure_S4A_middle_cell.hdf and Figure_S4B.hdf
File: alpha_tubulin_radial_density_profile.ipynb
Description: For Radial Projection in Figure_3H.hdf, Figure_3I.hdf, Figure_S4A_middle_cell.hdf and Figure_S4B.hd
File: Figure_3G.xlsx
Description: Comparison of spindle width in WT vs INPP4b cells
Variables
- Spindle Width (1st column-WT, 2nd column-INPP4B KD) (um)
File: Figure_2EF-WT.xlsx
Description: FBP17 and Tks4 Wave periods in WT cells
Variables
- Channel 1: Intensity
- Time interval (seconds)
File: Figure_4DEFG.xlsx
Description: Comparison of wave periods in cells undergoing unchanged mitotic wave periods vs changing mitotic wave periods
Variables
- Wave Period (seconds)
- Cell size (um2)
File: Figure_6C.xlsx
Description: Wave period in cells after BFA treatment
Variables
- Time : 1st column (seconds)
- Intensity: 2nd column
File: Figure_6D.xlsx
Description: Wave period in cells after Golgicide A treatment
Variables
- Time : 1st column (seconds)
- Intensity: 2nd column
File: Figure_6E.xlsx
Description: Wave period in cells after H89 treatment
Variables
- Time : 1st (seconds)
- Intensity: 2nd column
File: Figure_4C_wave_H2B_cluster.xlsx
Description: Wavelet analysis of a cell undergoing changing mitotic wave periods
Variables
- Intensity of Cdc42 BD-GFP: "channel 1" tab
- Intensity of H2B: "channel 2" tab
- Intensity of Cluster: "channel 3" tab
File: Figure_1E.xlsx
Description: Scatterplot of mitotic wave period vs basal area
Variables
- Basal Area: 1st Column (um2)
- Period: 2nd Column (seconds)
File: Figure_3C.xlsx
Description: Scatterplot of mitotic spindle length vs basal area
Variables
- Basal Area: 1st Column (um2)
- Length: 2nd Column (um)
File: Figure_6F.xlsx
Description: Scatterplot of changing wave periods in cells treated -/+ Golgicide A, BFA or H89 treatment
Variables
- Period (1st row indicate mitotic stage) (seconds)
- Cell size (um2)
- Tabs (under indicate treatment)
File: All .hdf files
Description: .hdf files contain processed DNA-PAINT super-resolution point cloud datasets.
To visualize these files, install the PYthon Microscopy Environment (PYME) software package and open the datasets using the PYMEVisualize application.
Backticks around filenames and software commands are used to format as inline code.
The PYME source code and installation resources are available from the official repository: https://github.com/python-microscopy/python-microscopy
Access information
These Excel files contain the source data used to generate the figures in the manuscript. Each file is organized to make it easy to identify the parameters, experimental conditions, and measurements shown in the corresponding figure panels.
1. Plot Data Files
- The first (top) row of each sheet lists the parameters that were analyzed
- When multiple experimental conditions are included, they are separated into different tabs within the same Excel file. Each tab corresponds to one condition.
2. Intensity Plot Files
For all intensity plots except Figure 6C–E:
- Tabs labeled “Channel” correspond to the specific marker or fluorescent channel analyzed.
- The “Time” column indicates acquisition time (i.e., frame number or time in seconds, depending on the experiment).
- Tabs labeled “Info” provide additional details about the marker, imaging settings, or experimental context.
For Figure 6C–E:
- First tab:
- Column 1 — Acquisition time (seconds)
- Column 2 — Measured intensity values
- Second tab: Contains the corresponding period analysis used to quantify oscillatory behavior.
Changes after May 20, 2026:
The area and length values have been updated in the Figure 3E.xlsx file.
