Mapping-by-sequencing project - microscopy ARC
👋 Welcome to this bio-image ARC
The Content in Brief
This ARC contains content from the following publication:
In this ARC, you can find CLSM z-stacks acquired to analyze ARK1 cytoskeletal localisation and it's modulation upon treatment in leaf epidermal cells.
Tif files were extracted with metadata from lif files of respective CLSM sessions. Tif files were chosen as these are accessible without additional tools.
I would like to thank all colleagues and students involved by contributing help e.g. for cloning and plant care in the Huelskamp lab and at the Institute of Plant Science including the greenhouse team beyond the authors of the linked publication. 🚀
Description
The content of this ARC originates from the CLSM experimental part of a study which identified ARK1 with a mapping-by-sequencing approach to be causative for a root hair branching phenotype in only one Arabidopsis thaliana accession out of an accession panel.
It is intended to serve as a microscopic, bio-imaging use cases and initial example ARC for further development and conversion steps of ARCs with other microscopy-related studies and structures.
In the overarching mapping-by-sequencing project, we developed a strategy for Arabidopsis thaliana studies using different natural accessions to identify causative genes for distinct phenotypes. In these studies, an interesting phenotype can be found which is only represented by one or a few accessions. While the method of mapping-by-sequencing was developed already earlier, this study focusses on complementing GWAS studies for theses specific cases of low statistical power for causal gene detection in order to identify also genes underlying phenotypes of interest to a study with a low minor allele frequency in the panel. It makes use of three crossing instead of one in order to significantly reduce the mapping interval and uses additional information from the mapping panel and its respective sequences provided by the 1001 Genome Project.
For more details, please see the respective publication!
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| The logo of this ARC shows YFP-ARK1 in an A. thaliana leaf epidermal cell upon biolistic transformation with an YFP-ARK1 construct. (image: CC-BY 4.0: Andrea Schrader) |
Authors
Work included in this ARC is described in the related article. The work in the related article was conducted by:
- Louai Rishmawi, affiliation: CEPLAS, University of Cologne
- Hequan Sun, affiliation: Max Planck Institute for Plant Breeding Research
- Korbinian Schneeberger, affiliation: Max Planck Institute for Plant Breeding Research
- Martin Hülskamp*, affiliation: CEPLAS, University of Cologne
- Andrea Schrader*, affiliation: University of Cologne,current affiliation: CEPLAS, University of Cologne
Contact and Corresponding* Authors
The contact person for this ARC is
- Andrea Schrader
The corresponding authors for the study described in the related manuscript are
- Andrea Schrader
- Martin Hülskamp
License
Content published in the related article underlies the respective license for this article.
This microscopy ARC has the CC-BY 4.0 license.
Funding
The mapping-by-sequencing project was part of work funded by
CRC680, CEPLAS & IMPRS This work was supported by CRC680 (to M.H.), the Cluster of Excellence on Plant Sciences (grant no. EXC 1028 to Martin Huelskamp and a fellowship to Louai Rishmawi), and the International Max Planck Research Schools (fellowship to Louai Rishmawi).
Creating this ARC (Andrea Schrader) is part of work funded by
CEPLAS
CEPLAS is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) within Germany´s Excellence Strategy – EXC-2048/1 – project ID 390686111.
🚧 Under Construction 🚧
Acknowledgment
tbc
Project status & Roadmap
This microscopy ARC is intended to serve as an example.
It contains already the relevant isa metadata and needs to be extended using the Swate tool for adding annotations for the included data and the respective experiment.