diff --git a/studies/R-geneDataSet/README.md b/studies/R-geneDataSet/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/R-geneDataSet/isa.study.xlsx b/studies/R-geneDataSet/isa.study.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..cc652d17f26b48e3556b032863e51784be39bd61 Binary files /dev/null and b/studies/R-geneDataSet/isa.study.xlsx differ diff --git a/studies/R-geneDataSet/protocols/.gitkeep b/studies/R-geneDataSet/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/R-geneDataSet/protocols/R-geneData.md b/studies/R-geneDataSet/protocols/R-geneData.md new file mode 100644 index 0000000000000000000000000000000000000000..33cb4a2e826c54b7fcac432a0f4d1e7fe447b4a7 --- /dev/null +++ b/studies/R-geneDataSet/protocols/R-geneData.md @@ -0,0 +1,3 @@ +## *R*-gene Data Set + +The lists of the *R*-gene repertoires of *S. lycopersicum* and *S. tuberosum* were retrieved from Jupe et al. (2013). *R*-genes were classified as “full-length†NBS-LRRs if they contained both NBS and LRR domains as identified using InterPro (Mitchell et al., 2019). A slightly modified pipeline as described by Jupe et al. (2013) was used to verify their novel *R*-genes (Figure S2). These novel *R*-genes were designated by the authors as *R gene discovery consortium (RDC)* genes. Using AUGUSTUS (version 3.3.1), a gene-prediction tool developed by Stanke et al. (2008), we analyzed these *RDC* genes for coding regions and searched for NBS and LRR domains using InterPro. *RDCs* were classified as true *R*-genes if they possessed a coding region and an NBS-LRR domain. Otherwise they were excluded from further analysis. In cases in which multiple splice variants were identified, the longest splice variant was analyzed. The well-established *R*-genes *Pto* (Martin et al., 1993) and *EDS1* (Hu et al., 2005) from tomato were included in the dataset. In total, the expression patterns of 359 *R*-genes of tomato and 581 *R*-genes of potato were analyzed. \ No newline at end of file diff --git a/studies/R-geneDataSet/resources/.gitkeep b/studies/R-geneDataSet/resources/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391