# ARC mininmal Example RNASeq

This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations. 

## Data origin
- Partly published under: https://doi.org/10.1104/pp.15.01076
- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details. 

## Additional payload
> The following folders are not part of the ARC  
> for details, see: [ARC specs:Additional paylod](https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#additional-payload)

Directory | Purpose
---- | ----
[_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO


## Notes and ToDos

### Experimental metadata in isa.assay.xlsx
- split GEO SWATE templates into four sheets 
    - 1SPL01_plants
    - 2EXT01_RNA
    - 3ASY01_RNASeq
    - 4COM01_RNASeq

### Adding large raw data via git lfs 

1. Before addind the files to the ARC, track them via `git lfs`

```
git lfs track "*.fastq.gz"
git lfs track "01_kallisto_index"

```

2. Move / add the large data files to the respective folders

3. Add them via `git add`

```
git add assays/Talinum_RNASeq_minimal/dataset/
git add runs/run1/01_kallisto_index

```

4. Commit