Plant protoplasts display phytopodia

The raw data presented here relate to the publication# Plant protoplasts display phytopodia 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: [e-mail], [e-mail] § Equal contribution ORCIDs:* Johanna E. M. Dickmann: 0000-0002-0861-4440* Claire Lionnet: 0009-0000-0117-2507* Zoe Nemec-Venza: 0000-0002-2346-2596* Olivier Hamant: 0000-0001-6906-6620 published in Nature Communications in 2026 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 of 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 (or the Airyscan processed data for Airyscan images), 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 README folder for information on which exact file is displayed 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”, "Marjo-yyyymmdd") * the line of the imaged plant material (e.g. “pUBQ10-LTi6a-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 0.5 ug/ml) * sometimes information on a treatment (e.g. “beforeFDA” = image taken before FDA was added; “FDA2.5ugPml” or “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) * if applicable, information on the drug used ("DMSO" = control, "Taxol", "LatB" = LatrunculinB, "Oryzalin") * sometimes information on the 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 Airyscan images, information of the mode of Airyscan: "AiryscanMPLX" = Airyscan multiplex, "AiryscanSR" = super resolution Airyscan"; as well as on the processing: "2DAiryscanProcessing" = Airyscan processing in 2D, i.e. only using the information of the current z-plane or "3DAiryscanProcessing" = Airyscan processing in 3D, i.e. also taking into consideration information from neighbouring z-planes; the 3D option was only used if the z-spacing was chosen to be optimal for Airyscan imaging. In experiments in which Airyscan images were acquired, the additional images acquired at confocal resolution are explicitly labelled as "confocal". * for Fig. 1a: information about the length of the plasmolysis (“50 min”) * for Fig. 5a,b: information on which solution the protoplasts 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. 5c,d: 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. * for Fig.6f-h: In each experimental repeat folder, there are one or two folders with the technical repeats of that experiment. Sometimes, the alginate concentration is indicated "2_8percentAlginate" = 2.8 percent alginate. "beforeCaCl2" refers to images acquired before CaCl2 addition, "afterCaCl2" to images acquired after CaCl2 addition. * for SI_Fig.19: "afterCaCl2" = after addition of CaCl2; "afterMannitol" = after addition of Mannitol" (and equivalently for "before") ### 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 * sometimes 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, Calcofluor0.1P = Calcofluor 0.1 percent, FDA2.5ugPml = FDA 2.5ug/ml) * 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) * SI_Fig.6: Within each folder of an experimental repeat, the data are organised in folders by experimental day: "d0" = day of protoplasting, "d7" = after regenerating in the incubator for 7 days (sometimes noted as "incubator"). Within these, there are folders with the technical repeats ("dish1") of that day. These information also are part of the file names. ### Zea mays experiments The filenames contain the following information, separated by underscores or dashes:* the date on which the experiment was performed (yyyymmdd) * the plant species (“Maize”) * sometimes information on the solution used for digestion ("A+E" = hyperosmotic buffer solution with D-mannitol containing digestion enzymes) ### Bead experiments The filenames contain the following information, separated by underscores or dashes:* an experiment identifier (e.g. “beads008”) * a description of the beads (“fluoresbrite1micron” = Fluoresbrite beads of a diameter of 1 um) * sometimes information on the technical repeats ("dish1", "dish2") * an indication whether protoplasts and beads were mixed before imaging: "ProtosLTi6aTomato&Beads" or imaged separately "onlyBeads" or "proto" * 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.) * sometimes information on the size of the field of view (e.g. “small FOV” = small field of view, i.e. one microwell with beads) * sometimes 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”)