diff --git a/README.md b/README.md index 0535daaa08386c04a4c7a622efceb5e93cfc50a5..940be411ce92e43af114a474fd0280e580360f1b 100644 --- a/README.md +++ b/README.md @@ -1,42 +1,68 @@ -README template suggestion from https://git.nfdi4plants.org/kMutagene/validation_packages_test_index - Kevin Schneider @kMutagene +# Mapping-by-sequencing prject - microscopy ARC -# Editing this README +[](https://creativecommons.org/licenses/by/4.0/) -When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template. +## :wave: Welcome to this bio-image ARC -## Suggestions for a good README -Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information. +<br> -## Name -Choose a self-explaining name for your project. +## The Content in Brief + +This ARC contains content from the following publication: + +[Rapid Identification of a Natural Knockout Allele of ARMADILLO REPEAT-CONTAINING KINESIN1 That Causes Root Hair Branching by Mapping-By-Sequencing](https://doi.org/10.1104/pp.114.244046). + +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. + +<br> + +--- + +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](https://doi.org/10.1104/pp.114.244046). :rocket: + +--- + +<br> ## Description -Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors. -## Badges -On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge. +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. -## Visuals -Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method. +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. -## Installation -Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection. +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. -## Usage -Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README. +For more details, please see the respective [publication](https://doi.org/10.1104/pp.114.244046)! -## Support -Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc. -## Roadmap -If you have ideas for releases in the future, it is a good idea to list them in the README. -## Contributing -State if you are open to contributions and what your requirements are for accepting them. +<br> -For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self. -You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser. +| <img src="./studies/ARK1-cytoskeletal-localisation/resources/Logo-ARK1long-pENSG-YFP-in-Col-0.png" width="200" height="200" /> | +|:--:| +| *The logo of this ARC shows YFP-ARK1 in an *A. thaliana* leaf epidermal cell upon biolistic transformation with an YFP-ARK1 construct.* | + + +## Funding + +*The mapping-by-sequencing project was part of work funded by* + +**CRC680, CEPLAS & IMPRS** +This work was supported by [CRC680](http://www.sfb680.uni-koeln.de/index5.html) (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. + + +## :construction: Under Construction :construction: + +## Roadmap +If you have ideas for releases in the future, it is a good idea to list them in the README. ## Authors and acknowledgment Show your appreciation to those who have contributed to the project. diff --git a/studies/ARK1-cytoskeletal-localisation/resources/Logo-ARK1long-pENSG-YFP-in-Col-0.png b/studies/ARK1-cytoskeletal-localisation/resources/Logo-ARK1long-pENSG-YFP-in-Col-0.png new file mode 100644 index 0000000000000000000000000000000000000000..e4a3b4bc1d9da98d7768ca99444b1eeb70d95313 Binary files /dev/null and b/studies/ARK1-cytoskeletal-localisation/resources/Logo-ARK1long-pENSG-YFP-in-Col-0.png differ