zenodoopen

Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells

The raw data presented in this folder corresponds to the publication # Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells Johanna E. M. Dickmann 1,2, Marjolaine Martin 1,§, Claire Lionnet 1,§, Zoe Nemec-Venza 1, Olivier Hamant 1,2 1 Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, INRAE, CNRS, UCBL1   2 Correspondence: olivier.hamant@ens-lyon.fr, johanna.dickmann@ens-lyon.fr   § Equal contribution   ORCIDs: * Johanna Dickmann: 0000-0002-0861-4440 * Zoe Nemec-Venza: 0000-0002-2346-2596 * Olivier Hamant: 0000-0001-6906-6620 Submitted to bioRxiv in November 2024   This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 521501033 to J.D. and the European Research Council (ERC-2021-AdG-101019515 “Musix” to O.H.). ## Data organization The data are organized according to the figure panels in the publication. For large experiments, the folders may contain subfolders for each experimental repeat and/or condition. For explanations on the data and the methods, please refer to the publication. All data presented here are the original raw data output of the microscopes in the CZI format, a proprietary format developed by Zeiss, encapsulating both 4D image data and metadata, i.e. acquisition settings. This format is supported by open-source software such as Fiji and Open Microscopy Environment. Refer to the README files in the subfolders for information on which exact file was used to display in the figure. ## Explanation of the file names ### Arabidopsis experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g.”PLA001”, “PRO077”) * the line of the imaged plant material (e.g. “pUBQ10-LTi6B-TdTomato”) * sometimes information on the ecotype of the line (e.g. “Col-0”) * the age of the plants (e.g. “7d” = 7 day old plants) * sometimes information on a stain added (e.g. “FM4-64_0_5ugPml” = FM4-64 dye at a final concentration of 5 ug/ml) * sometimes information on a treatment (e.g. “beforeFDA” = image taken before FDA was added; “FDA2.5ugPml” = after adding FDA at a final concentration of 2.5 ug/ml, sometimes with additional information on the time between adding the FDA and imaging, e.g. “25min”) * sometimes information on the centrifugation speed (e.g. “100g”) * sometimes information on the imaging support (e.g. “bucket” = NOA73 container, “wells” = NOA73 microwells, “coverslip”) * sometimes information on the imaging mode (“z-stack”, “t-series” = time series/timelapse, “6x” = zoom of 6 in Zen software) * the solution the sample was imaged in (“Solution A” or “A” = hyperosmotic buffer with D-mannitol, “AS” = hyperosmotic buffer with D-sorbitol) * sometimes information on experimental setup (“ON” = overnight timelapse imaging) * increasing numbers at the end of the file name indicate subsequent fields of view or positions imaged with the same settings * for Fig. 1A: information about the length of the plasmolysis (“50 min”) * for Fig. 4c,d: information on which solution the protoplasts are and have been imaged in: “A” = hyperosmotic buffer solution with 600 mM D-mannitol. “B” =  hyperosmotic buffer solution with 280 mM D-mannitol. Times indicate time between addition of new buffer and onset of imaging of the position list. * for Fig. 4e-f: the concentration of the hyperosmotic buffer solution is indicated. For the control, the number of additions of hyperosmotic buffer solution with 600 mM D-mannitol is indicated. ### Physcomitrium patens experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g. "PyP001")   * “Physco_wt” referring to Physcomitrium patens wild type * the age of the moss tissue used for protoplasting (e.g. “6d” = 6 days) * information on the stain added (e.g. “ Fm4-64_2ugPml” = FM4-64 dye at a final concentration of 2 ug/ml) * information on the imaging support (e.g. “bucket” = NOA73 container, “coverslip”) ### Maize experiments The filenames contain the following information, separated by underscores: * the date on which the experiment was performed (yyyymmdd) * the plant species (“Maize”) * sometimes information in the solution used for digestion ("A+E" = hyperosmotic buffer solution with D-mannitol) ### Bead experiments The filenames contain the following information, separated by underscores: * an experiment identifier (e.g. “beads008”) * a description of the beads (“fluoresbrite1micron” = Fluoresbrite beads of a diameter of 1 um) * sometimes a short description of the protocol (e.g. “SolAwashed-2-3mLsolA” = NOA73 microwells were washed in hyperosmotic buffer with 600 mM D-mannitol 2x prior to imaging, beads were imaged in 3 ml hyperosmotic buffer solution with 600 mM D-mannitol.) * an information on the size of the field of view (e.g. “small FOV” = small field of view, i.e. one microwell with beads) * information at which approx. height of the microwell the image was taken (“TopOfWells” = close to the opening of the wells on the top) * sometimes information on the zoom of the Zen software (e.g. “7x”)

ShareScore

36/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 12
Reuse readiness: 8
Engagement: 4

Topics

plant cell biology protoplasts protrusions Hechtian structure

Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells

Score breakdown

Topics

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