# Facultative CAM in Talinum

:bulb: Check out the [wiki](https://git.nfdi4plants.org/brilator/samplearc_rnaseq/-/wikis/home) to this project for more information.

## Data origin

- see [isa.investigation.xlsx](./isa.investigation.xlsx) for details
- Adapted from
    > 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 -->
<!-- 
![](_workflow_scheme/workflow-scheme.drawio.png) -->

## 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

```