# 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
```