diff --git a/README.md b/README.md index 77b17a4d4533ec899b166146579ac6c7942ea56f..03e84e3d702ff73ab0776b9b90467815b28f0300 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,98 @@ > Brilhaus, D., Bräutigam, A., Mettler-Altmann, T., Winter, K., and Weber, A.P.M. (2016). Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in *Talinum triangulare*. Plant Physiology 170: 102–122. https://doi.org/10.1104/pp.15.01076 - [studies/TalinumGenomeDraft](./studies/TalinumGenomeDraft) originates from https://git.nfdi4plants.org/hhu-plant-biochemistry/talinum-fruticosum-genome -## RNASeq Workflow overview +<!-- ## RNASeq Workflow overview --> +<!-- + --> - \ No newline at end of file +## Sample Flow Overview + +```mermaid +graph LR; + +style studies/TalinumFacultativeCAM fill:#b4ce82 + +style assays/Talinum_RNASeq_minimal fill:#ffc000 +style assays/GCqTOF_targets fill:#ffc000 + +subgraph studies/TalinumFacultativeCAM + + DB_097 --[plant_material.md]--> CAM_01 + DB_099 --[plant_material.md]--> CAM_02 + DB_103 --[plant_material.md]--> CAM_03 + DB_161 --[plant_material.md]--> reC3_01 + DB_163 --[plant_material.md]--> reC3_02 + DB_165 --[plant_material.md]--> reC3_03 +end + +subgraph assays/Talinum_RNASeq_minimal + + CAM_01 --[rna_extraction.md]--> CAM_01_ext + CAM_02 --[rna_extraction.md]--> CAM_02_ext + CAM_03 --[rna_extraction.md]--> CAM_03_ext + reC3_01 --[rna_extraction.md]--> reC3_01_ext + reC3_02 --[rna_extraction.md]--> reC3_02_ext + reC3_03 --[rna_extraction.md]--> reC3_03_ext + + CAM_01_ext --[illumina.md]--> DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz + CAM_02_ext --[illumina.md]--> DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz + CAM_03_ext --[illumina.md]--> DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz + reC3_01_ext --[illumina.md]--> DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz + reC3_02_ext --[illumina.md]--> DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz + reC3_03_ext --[illumina.md]--> DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz +end + +subgraph assays/GCqTOF_targets + + CAM_01 --[metabolite_extraction.md]--> DB23 + CAM_02 --[metabolite_extraction.md]--> DB24 + CAM_03 --[metabolite_extraction.md]--> DB26 + reC3_01 --[metabolite_extraction.md]--> DB39 + reC3_02 --[metabolite_extraction.md]--> DB40 + reC3_03 --[metabolite_extraction.md]--> DB41 + + Std.Mix5µM --[gas_chromatography.md]--> 150112_03 + Std.Mix5µM --[gas_chromatography.md]--> 150112_04 + blank1 --[gas_chromatography.md]--> 150112_15 + blank1 --[gas_chromatography.md]--> 150112_16 + DB23 --[gas_chromatography.md]--> 150112_55 + DB23 --[gas_chromatography.md]--> 150112_56 + DB24 --[gas_chromatography.md]--> 150112_61 + DB24 --[gas_chromatography.md]--> 150112_62 + DB26 --[gas_chromatography.md]--> 150112_65 + DB26 --[gas_chromatography.md]--> 150112_66 + Std.Mix5µM --[gas_chromatography.md]--> 150115_03 + Std.Mix5µM --[gas_chromatography.md]--> 150115_04 + DB39 --[gas_chromatography.md]--> 150115_11 + DB39 --[gas_chromatography.md]--> 150115_12 + DB40 --[gas_chromatography.md]--> 150115_13 + DB40 --[gas_chromatography.md]--> 150115_14 + DB41 --[gas_chromatography.md]--> 150115_15 + DB41 --[gas_chromatography.md]--> 150115_16 + blank2 --[gas_chromatography.md]--> 150115_25 + blank2 --[gas_chromatography.md]--> 150115_26 + + 150112_03 --[mass_spec.md]--> 150112_03.D + 150112_04 --[mass_spec.md]--> 150112_04.D + 150112_15 --[mass_spec.md]--> 150112_15.D + 150112_16 --[mass_spec.md]--> 150112_16.D + 150112_55 --[mass_spec.md]--> 150112_55.D + 150112_56 --[mass_spec.md]--> 150112_56.D + 150112_61 --[mass_spec.md]--> 150112_61.D + 150112_62 --[mass_spec.md]--> 150112_62.D + 150112_65 --[mass_spec.md]--> 150112_65.D + 150112_66 --[mass_spec.md]--> 150112_66.D + 150115_03 --[mass_spec.md]--> 150115_03.D + 150115_04 --[mass_spec.md]--> 150115_04.D + 150115_11 --[mass_spec.md]--> 150115_11.D + 150115_12 --[mass_spec.md]--> 150115_12.D + 150115_13 --[mass_spec.md]--> 150115_13.D + 150115_14 --[mass_spec.md]--> 150115_14.D + 150115_15 --[mass_spec.md]--> 150115_15.D + 150115_16 --[mass_spec.md]--> 150115_16.D + 150115_25 --[mass_spec.md]--> 150115_25.D + 150115_26 --[mass_spec.md]--> 150115_26.D + +end + +```