Supplemental data to "A mechanical ratchet drives unilateral cytokinesis"
Contributing person | Jan Brugues | |
Contributing person | Alison Kickuth | |
Contributing person | Ursa Ursic | |
References to related material | Publication "A mechanical ratchet drives unilateral cytokinesis" by Alison Kickuth, Urša Uršič, Michael F. Staddon, and Jan Brugués. | |
Description of the data | The uploaded data contains subfolders according to each figure and supplementary figure of the paper. Detailed descriptions of the data for the main figures is provided here. Figure 1a Title: Contractile band formation Authors: Alison Kickuth Description: Zebrafish (D. rerio) embryos during the first cell division. Maximum intensity projection of actin (labelled by utrophin-mCherry), and microtubules (labelled by DCX-GFP). Pixel size 1.08 um. More imaging detailed available in attached txt file. Figure 1b Title: High resolution contractile band formation Authors: Alison Kickuth Description: Maximum intensity projection of embryo labelled for actin and microtubules visualising the band formation at high resolution (40x magnification, spinning disk confocal). Figure 1d Title: Laser ablation on contractile actin band Authors: Alison Kickuth Description: Single confocal imaging plane of the embryo with contractile band during continuous laser ablation (labelled for DCX-EGFP and utrophin-mCherry). Pixel size 0.18 um, time interval 300 ms, more imaging details in attached txt file. Figure 1e Title: Contractile band recoil from laser ablation and actin grey values Authors: Alison Kickuth Description: Data of 4 embryos (and corresponding metadata in txt), corresponding to the plot shown in Figure 1e of “A mechanical ratchet drives unilateral cytokinesis”. Only the first cut per embryo was considered. For the plot, a line was drawn across the cut opening, and the band length as well as actin grey value were plotted. Figure 2a Title: Contractile band laser ablation and microtubules Authors: Alison Kickuth Description: Laser cut on the contractile actin band, actin and microtubules imaged with confocal spinning disk microscopy, pixel size 0.2 um, 300 ms time interval. Figure 2b Title: Contractile band laser ablation and microtubule orientation (manual detection) Authors: Alison Kickuth Description: Raw data corresponding to microtubule orientation measurements shown in Fig2b, as well as measurements from Fiji and python code for plotting the microtubule angles. Figure 2c Title: Contractile band laser ablation and microtubule orientation (automatic detection) Authors: Alison Kickuth Description: Raw data corresponding to microtubule angle change over time shown in Fig2c. Raw data, microtubule angle measurements (from Fiji plugin OrientationJ), and mathematica code for plotting angles. Readme file in measurements folder explains settings for obtaining angles from OrientationJ. Figure 2d Title: Microtubule depolymerization during first cell division of zebrafish embryo Authors: Alison Kickuth Description: Zebrafish embryo (top view) treated with SbTubA4P, a photoactivatable microtubule inhibitor. Flash of light indicates inhibitor photoactivation (405 nm with DMD). 30s time interval, 0.39 um pixel size. Figure 2e Title: Contractile band regression velocity in microtubule depolymerized and interphase arrested embryos. Authors: Alison Kickuth, Michael Staddon Description: Contractile band regression velocity in microtubule depolymerized (SbTub) and interphase arrested (CHX) embryos corresponding to Fig2a. Folder contains data for all measured embryos (in separate folders according to treatment), showing microscopy images as well as measurements obtained from PIV and individual PIV settings. Code for plotting PIV data is available on the provided Github by Michael Staddon. Figure 2g Title: Obstacle in embryo cytoplasm disrupting actin band Authors: Alison Kickuth Description: Embryo (top view) during first cell division, the contractile band is interrupted through an obstacle in the cytoplasm (visible in actin and microtubule channel). Time interval 15s, pixel size 0.39 um. The obstacle consists of a fluorescent oil droplet. Figure 3a Title: Interphase arrested zebrafish embryo at 1-cell stage Authors: Alison Kickuth Description: Embryo (side view) treated with cycloheximide to arrested in interphase of the first cell division. 15s time interval. Folder contains raw data (3d stacks, saved in 2GB files) as well as maximum intensity projections. Figure 3b Title: Microtubule depolymerization in interphase arrested 1-cell stage zebrafish embyro Authors: Alison Kickuth Description: Embryo treated with cycloheximide to arrest in interphase as well as SbTubA4P to depolymerise microtubules upon photoactivation. Raw data is split into “pre-activation” and “post-activation”. Photoactivation occurred between the two by taking a single z-stack of the sample with 405 nm illumination. Maximum intensity projection shows compiled time course, time interval 60s. Figure 3 d-h Title: Magnetic tweezers measurements in zebrafish embryo cytoplasm Authors: Alison Kickuth, Urša Uršič Description: Folder contains all raw data for unperturbed embryos, as well as treated embryos in a separate folder (taxol and nocodazole). For every imaged embryo, a brightfield image was taken to show the location of the tip. A z-stack was taken before the measurement and after the measurement to better visualize microtubule morphology, and a single z-plane was imaged throughout the magnetic tweezers measurement with 500 ms time interval. The corresponding code for analysing the data is available on github. Figure 3h Title: Optical tweezer measurements in zebrafish embryo cytoplasm Authors: Alison Kickuth, Urša Uršič, Jan Brugués Description: Optical tweezers data corresponding to optical tweezers measurements shown in figure 3h. The data folder contains both the raw optical tweezers measurements as well as the microscopy data taken during a measurement, showing cell cycle stage as well as location of the measured bead. The measurements folder contains the exported measurements as excel file. Figure 4a Title: Ingression of the contractile actin band Authors: Alison Kickuth, Michael Staddon Description: Ingression of the contractile band over time manually measured from confocal microscopy images of zebrafish embryos measured through their chorion (To avoid confinement in agarose). The “0_data” folder contains the raw imaging data that was measured, as well as the corresponding metadata. The “1_measurements” folder contains the measurements of the location of the ingression front (ing) as well as the highest point of the cortex that was measured for reference (ref). The “2_code” folder contains the code and information for generating the shown plot in Fig 4a (including simulation result by Michael Staddon). Figure 4b Title: Contractile band ingression kymograph Authors: Alison Kickuth Description: Ingression of the contractile band, showing how the furrow ingresses, the ingression is slightly reversed in M-phase, the ingression pauses in the next interphase, and continues in the next M-phase. Maximum intensity projection showing actin, microtubules and membrane (albeit not very good staining). A second folder provides the projection from only the z-slices used to generate the image shown in figure 4b. Figure 4c Title: Laser ablation within contractile band Authors: Alison Kickuth Description: Data showing laser ablation within the band (meaning it is not cut through entirely, actin band remains on all sides of the cut). The “0_data” folder contains all raw microscopy data and metadata. The “1_measurements” folder contains kymographs made across the laser cuts as well as the measurements extracted from kymograph contours in python. The “2_code” folder contains all iterations of the code to extract and fit the kymograph contours, as well as the code for plotting the retraction velocity. The “3_pipeline” folder contains the code used to extract and plot the data shown in Fig4c as well as a readme file explaining the data analysis procedure. The “4_plots” folder contains all iterations of plots. Figure 4d Title: Laser ablation within contractile band (related to 4c) Authors: Alison Kickuth Description: Fig 4d is related to Fig4c. The corresponding folder contains only a readme file, referring the reader to the folder for Fig4c, which contains all the raw data. Figure 4f Title: Actin band ingression velocity with microtubule depolymerisation Authors: Alison Kickuth Description: The folder for Fig4f contains the following subfolders: “0_data” and “1_measurements”. The data folder contains the raw microscopy data, metadata and maximum intensity projections (used for analysis). The measurements folder contains the ingression velocity measurements obtained from manual tacking. In this case, no reference files were used (unlike in fig 4a), because the measured embryos were confined in agarose and this did not move/deform as much. The authors confirm that the confinement in agarose does not affect the ingression velocity (as shown in supplementary figure 5 of the paper). | |
Type of the data | Dataset | |
Type of the data | Image | |
Total size of the dataset | 376872952006 | |
Author | Kickuth, Alison | |
Author | Ursic, Urša | |
Author | Staddon, Michael Feroli | |
Author | Brugués, Jan | |
Upload date | 2025-10-01T09:26:47Z | |
Publication date | 2025-10-01T09:26:47Z | |
Data of data creation | 2025 | |
Publication date | 2025-10-01 | |
Abstract of the dataset | This dataset presents raw imaging data, quantitative measurements, and data visualisation code from zebrafish embryo experiments investigating contractile band dynamics during early cell division. The study examines the mechanical processes that drive unilateral cytokinesis, focusing on cytoskeletal organization across the cell cycle. High-resolution time-lapse microscopy and quantitative image analysis were used to capture and assess the cellular behaviours. | |
Public reference to this page | https://opara.zih.tu-dresden.de/handle/123456789/1702 | |
Public reference to this page | https://doi.org/10.25532/OPARA-947 | |
Publisher | Technische Universität Dresden | |
Licence | Attribution-NonCommercial-NoDerivatives 4.0 International | en |
URI of the licence text | http://creativecommons.org/licenses/by-nc-nd/4.0/ | |
Specification of the discipline(s) | 2::21::201::201-02 | |
Specification of the discipline(s) | 2::21::201::201-03 | |
Specification of the discipline(s) | 2::21::201::201-06 | |
Title of the dataset | Supplemental data to "A mechanical ratchet drives unilateral cytokinesis" | |
Research instruments | Zeiss Light Sheet Z.1, lateral illumination and detection geometry, equipped with 2 PCO edge 5.5m, monochrome sCMOS cameras (SN 61000966, 61004862) for detection. Imaged with Zeiss Plan Apo 20x (1.0 NA) Water DIC objective. Controlled through Zeiss ZEN 2014 SP1 9.2.10.54 software. | |
Research instruments | Spinning disk confocal Andor Revolution platform with Borealis extension, Andor IX 83 inverted stand, Yokogawa CSU-W1 scan head, equipped with an Olympus silicone oil-immersion objective (30x/1.08 U Plan SApo, Silicone, OLYMPUS), or air objective (Olympus UplanXApo 20x/0.80 Air), recording with simultaneous imaging of two fluorophores with two Andor iXon Ultra 888, Monochrome EMCCD cameras (dexel size 13 µm) | |
Research instruments | Spinning disk confocal Nikon Ti Eclipse, Yokogawa CSU-X1, equipped with a back-illuminated EMCCD camera (iXon DU-888 or DU-897, Andor) and a 60x water-immersion objective (Nikon Plan Apo VC 60x WI, NA 1.2) for laser ablation and optical tweezers, as well as 20x objective (Nikon Plan Apo 20x air, NA 0.75) for magnetic tweezers. Image acquisition was controlled by Andor iQ software in laser ablation and magnetic tweezer experiments, and through Nikon NIS-Elements software for optical tweezer experiments, as well as laser ablation shown in Fig 2a. | |
Research instruments | Nikon Ti Eclipse microscope body using epifluorescence imaging through a 20x air, NA 0.5 objective, recorded with a Hamamatsu Flash 4.0 camera, controlled through µManager software | |
Research instruments | Ti:Sapphire laser (Coherent Chameleon Vision II) ablation laser | |
Research instruments | Impetux, SENSOCELL optical tweezers setup | |
Underlying research object | Danio rerio | |
Project abstract | The uploaded data corresponds to the publication "A mechanical ratchet drives unilateral cytokinesis" by Alison Kickuth, Urša Uršič, Michael F. Staddon, and Jan Brugués. The paper describes the physical mechanism of unilateral cytokinesis. Specifically, the first cell division in zebrafish embryos (as an example of unilateral cytokinesis). The paper describes that in this case, no contractile ring is formed, but only a partial ring or contractile band. Further, it shows the anchoring mechanism of the contractile band and how the ingression is possible. The conclusion is that the cell division in completed through a "ratchet mechanism". The data is structured into subfolders according to their corresponding figure in the paper. | |
Project title | A mechanical ratchet drives unilateral cytokinesis |
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