ARC minimal Example RNASeq

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

Data origin

• see ./isa.investigation.xlsx for details.
• Published under: https://doi.org/10.1104/pp.15.01076

Setting up the arc structure using arcCommander

# initialize the structure
arc init 

# set up investigation 
arc i create --identifier samplearc_rnaseq 

# add study folders to place input material and data
arc study add -s TalinumFacultativeCAM 
arc study add -s TalinumGenomeDraft

# add assay folder to place assay data
arc assay add -s TalinumFacultativeCAM -a Talinum_RNASeq_minimal

Describe experiments using SWATE

File	Selected swate template
studies/TalinumFacultativeCAM/isa.study.xlsx	"Plant growth" v. 1.1.2
assays/Talinum_RNASeq_minimal/isa.assay.xlsx	"RNA extraction" v. 1.1.6 "RNA-Seq Assay" v. 1.1.7

Additional payload

The following folders are not part of the pure ARC
for details, see: ARC specs:Additional paylod

Directory	Purpose
_GEO_submission	Example metadata files as required for submission to GEO