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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: 2022-252-1. Version: 2. DOI: https://doi.org/10.5878/17te-jg54

Citation

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

Research principal

Swedish University of Agricultural Sciences - Department of Forest Genetics and Plant Physiology rorId

Principal's reference number

SLU.genfys.2023.4.4.IÄ-2

Description

The data set contains Tiff Z-stacks from light-grown hypocotyls and cotyledons 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).

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://doi.org/10.5281/zenodo.7436075).

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

Data contains personal data

No

Language

Method and outcome

Data format / data structure

Species and taxons

Arabidopsis thaliana

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
Geographic coverage
Administrative information

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: Mechanics and dynamics of cell-to-cell adhesion in plants
  • Funding information: Mekanik och dynamik av cell till cell adhesion i växter

Funding 2

  • Funding agency: VINNOVA rorId
  • Funding agency's reference number: 2016-00504
  • Project name on the application: UPSC Centre for Forest Biotechnology
  • Funding information: UPSC Centrum för Skogsbioteknik (UPSC)

Funding 3

  • Funding agency: Bio4Energy

Funding 4

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

Funding 5

  • Funding agency: Knut and Alice Wallenberg Foundation rorId
  • Funding agency's reference number: KAW 2016.0352
Topic and keywords

Research area

Cell biology (Standard för svensk indelning av forskningsämnen 2011)

Developmental biology (Standard för svensk indelning av forskningsämnen 2011)

Plant biotechnology (Standard för svensk indelning av forskningsämnen 2011)

Keywords

Ablation, Arabidopsis thaliana, Microtubule, Hypocotyl

Publications
SND Logo

License

CC BY 4.0

Versions

Version 2. 2023-05-10

Version 2: 2023-05-10

DOI: https://doi.org/10.5878/17te-jg54

File conversion: Repackage data files so files for each genotype are in a separate zip file, rather than everything in one very large zip file.

Data added: Added "Pavement cells.zip", update documentation file ReadMe_Experiment settings.txt and metadata. The first version of the data set contained images from time series experiment of acquired on hypocotyls of cortical microtubules reporter either with few or no ablated cells. The second version contains additional images of a time serie experiment on one cotyledon from a microtubule reporter line after ablating a few cells.

Version 1. 2023-02-24

Version 1: 2023-02-24

DOI: https://doi.org/10.5878/62ed-8017

Contact for questions about the data

Stéphane Verger

Stephane.verger@umu.se

Published: 2023-05-10
Last updated: 2023-11-16