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26 results for “protoplasts”
Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells
<p>The raw data presented in this folder corresponds to the publication<br># Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells</p> <p>Johanna E. M. Dickmann 1,2, Marjolaine Martin 1,§, Claire Lionnet 1,§, Zoe Nemec-Venza 1, Olivier Hamant 1,2</p> <p>1 Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, INRAE, CNRS, UCBL1 <br>2 Correspondence: olivier.hamant@ens-lyon.fr, johanna.dickmann@ens-lyon.fr <br>§ Equal contribution </p> <p>ORCIDs:<br>* Johanna Dickmann: 0000-0002-0861-4440<br>* Zoe Nemec-Venza: 0000-0002-2346-2596<br>* Olivier Hamant: 0000-0001-6906-6620</p> <p>Submitted to bioRxiv in November 2024 </p> <p>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.).</p> <p>## Data organization</p> <p>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.</p> <p>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.</p> <p>Refer to the README files in the subfolders for information on which exact file was used to display in the figure.</p> <p>## Explanation of the file names</p> <p>### Arabidopsis experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g.”PLA001”, “PRO077”)</p> <p>* the line of the imaged plant material (e.g. “pUBQ10-LTi6B-TdTomato”)</p> <p>* sometimes information on the ecotype of the line (e.g. “Col-0”)</p> <p>* the age of the plants (e.g. “7d” = 7 day old plants)</p> <p>* sometimes information on a stain added (e.g. “FM4-64_0_5ugPml” = FM4-64 dye at a final concentration of 5 ug/ml)</p> <p>* 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”)</p> <p>* sometimes information on the centrifugation speed (e.g. “100g”)</p> <p>* sometimes information on the imaging support (e.g. “bucket” = NOA73 container, “wells” = NOA73 microwells, “coverslip”)</p> <p>* sometimes information on the imaging mode (“z-stack”, “t-series” = time series/timelapse, “6x” = zoom of 6 in Zen software)</p> <p>* the solution the sample was imaged in (“Solution A” or “A” = hyperosmotic buffer with D-mannitol, “AS” = hyperosmotic buffer with D-sorbitol)</p> <p>* sometimes information on experimental setup (“ON” = overnight timelapse imaging)</p> <p>* increasing numbers at the end of the file name indicate subsequent fields of view or positions imaged with the same settings</p> <p>* for Fig. 1A: information about the length of the plasmolysis (“50 min”)</p> <p>* 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.</p> <p>* 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.</p> <p>### Physcomitrium patens experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g. "PyP001") </p> <p>* “Physco_wt” referring to Physcomitrium patens wild type</p> <p>* the age of the moss tissue used for protoplasting (e.g. “6d” = 6 days)</p> <p>* information on the stain added (e.g. “ Fm4-64_2ugPml” = FM4-64 dye at a final concentration of 2 ug/ml)</p> <p>* information on the imaging support (e.g. “bucket” = NOA73 container, “coverslip”)</p> <p>### Maize experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* the date on which the experiment was performed (yyyymmdd)</p> <p>* the plant species (“Maize”)</p> <p>* sometimes information in the solution used for digestion ("A+E" = hyperosmotic buffer solution with D-mannitol)</p> <p>### Bead experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g. “beads008”)</p> <p>* a description of the beads (“fluoresbrite1micron” = Fluoresbrite beads of a diameter of 1 um)</p> <p>* 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.)</p> <p>* an information on the size of the field of view (e.g. “small FOV” = small field of view, i.e. one microwell with beads)</p> <p>* information at which approx. height of the microwell the image was taken (“TopOfWells” = close to the opening of the wells on the top)</p> <p>* sometimes information on the zoom of the Zen software (e.g. “7x”)</p>
Supplemental Datasets for 'Multiplexed effector screening for recognition by endogenous resistance genes using positive defense reporters in wheat protoplasts'
<p>Supplemental Datasets:</p><p><strong>Number </strong></p><p><strong>File name </strong></p><p><strong>Description </strong></p><p>S1 </p><p>S1_Figure1_Data.csv </p><p>Luminescence data for Figure 1, protoplast time course experiment </p><p>S2 </p><p>S2_RNAseqSampleTable.csv </p><p>List of samples and treatment groups for RNAseq experiment </p><p>S3 </p><p>S3_LFC_1_genes.xlsx </p><p>Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 1 </p><p>S4 </p><p>S4_GOTerms_Table.xlsx </p><p>GO terms analysis Query tables and g:profiler results tables </p><p>S5 </p><p>S5_LFC2_genes.xlsx </p><p>Lists of Gabo/GaboSr50, Fielder and all cultivar genes upregulated by log fold threshold of 2 </p><p> </p><p>S6 </p><p>S6_Primers.xlsx </p><p>List of primers used </p><p>S7 </p><p>S7_PlasmidList.xlsx </p><p>List of plasmids used </p><p>S8 </p><p>S8_Figures3-5Data.xlsx </p><p>Luminescence data used for generating Figures 3 - 7</p><p>S9</p><p> </p><p>S9_Figures3-7Stat.xlsx</p><p> </p><p>Stats output for Figures 3 - 7</p><p> </p><p>S10</p><p> </p><p>S10_SuppFiguresData.xlsx</p><p> </p><p>Data for Supplementary Figures S1 and S2</p><p> </p>
mRNA changes following induction of GmWRI1 activity in Arabidopsis leaf mesophyll protoplasts
GEO Series GSE253107. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Bacterial Protoplast-Derived Nanovesicles Carrying CRISPR/Cas9 Tools Efficiently Re-educate Tumor-Associated Macrophages for Cancer Immunotherapy
GEO Series GSE243428. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Microarray analysis of scap1 mutant and wild type in Arabidopsis thaliana guard cell protoplast
GEO Series GSE43964. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
Protoplast data: suberized exodermis is required for tomato drought tolerance
GEO Series GSE212404. Solanum lycopersicum. 6 samples. Type: Expression profiling by high throughput sequencing.
Nitrogen and cycloheximide effects on protoplast and TF-target identification in the TARGET assay
GEO Series GSE128209. Arabidopsis thaliana. 46 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens
GEO Series GSE36117. Physcomitrium patens. 4 samples. Type: Expression profiling by high throughput sequencing.
Expression data from Arabidopsis thaliana root protoplast
GEO Series GSE69389. Arabidopsis thaliana. 11 samples. Type: Expression profiling by array.
Positive fluorescent selection permits precise, rapid and in-depth over-expression analysis in plant protoplasts
GEO Series GSE13783. Arabidopsis thaliana. 18 samples. Type: Expression profiling by array.
RNAseq of transfected protoplasts of Populus trichocarpa
GEO Series GSE154167. Populus trichocarpa. 9 samples. Type: Expression profiling by high throughput sequencing.
Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
GEO Series GSE10496. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Expression analysis of the effect of protoplasting and FACS sorting in roots
GEO Series GSE7636. Arabidopsis thaliana. 4 samples. Type: Expression profiling by array.
Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection
GEO Series GSE11217. Arabidopsis thaliana. 24 samples. Type: Expression profiling by array.
Expression analysis of the effect of protoplasting and sorting in roots exposed to low pH
GEO Series GSE30091. Arabidopsis thaliana. 5 samples. Type: Expression profiling by array.
transcriptome profiling from a protoplast culture of arabidopsis thaliana-From protoplast to plant : transcrip...
GEO Series GSE7984. Arabidopsis thaliana. 32 samples. Type: Expression profiling by array.
Arabidopsis protoplasts : TMV*rep vs. TMV*CP.MP transfected
GEO Series GSE45283. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Transcriptome Profiles of Differentiated arabidopsis Leaf Cells and Dedifferentiating Protoplasts of Ler and kyp mutant
GEO Series GSE15515. Arabidopsis thaliana. 7 samples. Type: Expression profiling by array.
Transcriptional responses to protoplasting in the early leaf developmental zone of Brachypodium distachyon
GEO Series GSE306756. Brachypodium distachyon. 6 samples. Type: Expression profiling by high throughput sequencing.
Beyond the protoplast: isolating and analyzing fixed cells for plant single-cell research
GEO Series GSE183422. Zea mays. 303 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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