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Dataset of confocal microscopy from plant samples - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress

SND-ID: 2022-252

Creator/Principal investigator(s)

Elsa Demes - Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology orcid

Stéphane Verger - Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology orcid

Description

The data set contains Tiff Z-stacks from light-grown hypocotyls of cortical microtubule (CMT) reporter lines either with few or no ablated cells from a time series experiment. This data set was analyzed with a new semi-automated image analysis workflow we have developed to quantify CMTs reorganization in individual cells following an ablation (https://github.com/VergerLab/MT_Angle2Ablation_Workflow).

Language

English

Research principal, contributors, and funding

Research principal

Swedish University of Agricultural Sciences

Principal's reference number

SLU.genfys.2023.4.4.IÄ-2

Responsible department/unit

Department of Forest Genetics and Plant Physiology

Funding 1

  • Funding agency: Swedish research council rorId
  • Funding agency's reference number: 2020-03974
  • Project name on the application: Starting grant

Funding 2

  • Funding agency: VINNOVA rorId
  • Funding agency's reference number: 2016-00504

Funding 3

  • Funding agency: Bio4Energy

Funding 4

  • Funding agency: Knut and Alice Wallenberg Foundation rorId
  • Funding agency's reference number: KAW 2016.0341 and KAW 2016.0352
Protection and ethical review

Data contains personal data

No

Method and time period

Species and taxons

arabidopsis thaliana

Geographic coverage
Topic and keywords

Research area

Cell Biology, Developmental Biology, Plant Biotechnology (The Swedish standard of fields of research 2011)

Keywords

ablation, arabidopsis thaliana, microtubule, hypocotyl

Publications
Dataset
Dataset of confocal microscopy from plant samples - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress

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Associated documentation

Description

The dataset in the zip file was analyzed using the scripts on GitHub (https://github.com/VergerLab/MT_Angle2Ablation_Workflow). A step by step describes and explains all the scripts of the image analysis procedure. The intermediate data generated by the analysis method can be found on zenodo (https://zenodo.org/record/7436075#.Y5rmd-zMJF8).

The documentation file Example_2D_Image.tif gives a visual representation from a typical z-stack.

Version 1

Citation

Elsa Demes, Stéphane Verger. Swedish University of Agricultural Sciences (2023). Dataset of confocal microscopy from plant samples - High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress . Swedish National Data Service. Version 1. https://doi.org/10.5878/62ed-8017

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Data format / data structure

Still image

3D

Creator/Principal investigator(s)

Elsa Demes - Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology orcid

Stéphane Verger - Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology orcid

Data collection

  • Mode of collection: Recording
  • Description of the mode of collection: Confocal microscope time series images of hypocotyls (every 20 minutes during 4 hours) were taken on microtubules reporter lines
  • Instrument: confocal microscope Zeiss LSM800 - Upright confocal microscope from Zeiss
  • Sample: GFP-MBD
    Fluorophore fused to a microtubule binding domain from the Microtubule Associated Protein 4 (MAP4). (Marc et al., 1998) DOI: 10.1105/tpc.10.11.1927
  • Sample: mCit-MBD
    Fluorophore fused to a microtubule binding domain from the Microtubule Associated Protein 4 (MAP4). (Armezzani et al., 2018) DOI: 10.1242/dev.162255
  • Sample: bot1-7 GFP-MBD
    GFP-MBD line crossed with bot1-7 a katanin mutant with impaired rearrangement of microtubules. (Uyttewaal et al., 2012) DOI: 10.1016/j.cell.2012.02.048
  • Sample: GFP-TUA6
    GFP fused to a tubulin subunit. (Ueda et al., 1999) https://doi.org/10.1007/BF01279267
  • Source of the data: Research data, Biological samples
  • Temporal resolution: 20 minute

License

Creative Commons Attribution 4.0 International (CC BY 4.0)

Contact for questions about the data

Stéphane Verger

Stephane.verger@umu.se

Published: 2023-02-24