update readme and protocols

README.md

@@ -2,6 +2,18 @@
 
 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
 
@@ -12,7 +24,6 @@ This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and co
     - 3ASY01_RNASeq
     - 4COM01_RNASeq
 
-
 ### Adding large raw data via git lfs 
 
 1. Before addind the files to the ARC, track them via `git lfs`
@@ -34,7 +45,3 @@ git add runs/run1/01_kallisto_index
 ```
 
 4. Commit
-
-## To Do's
-- CWL not yet implemented 
-

assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md

+```
+Note: 
+- This is a somewhat polished protocol as found in a publication. 
+- This is not an example for a typical lab protocol or method. 
+```
+
 # Plant Material and Growth Conditions
 
-Talinum triangulare plants were grown in Miracle-Gro Potting Mix (Miracle- Gro) in “Short-One” treepots, 1.6 l (Stuewe and Sons). The experiment was initiated with 28-d-old plants in a controlled environment chamber (Environ- mental Growth Chambers) maintained under 12 h light (30°C, 37% relative humidity)/12 h dark (22°C) cycles. Photon flux density at leaf level was 425 mmol m22 s21. Irrigation was withheld on day 1 and recommenced on day 14. Leaves were harvested when plants were well-watered as well as after 4, 9, and 12 d of water deprivation and watered for two days following the drought period.
+*Talinum triangulare* plants were grown in Miracle-Gro Potting Mix (Miracle-Gro) in “Short-One” treepots, 1.6 l (Stuewe and Sons). The experiment was initiated with 28-d-old plants in a controlled environment chamber (Environmental Growth Chambers) maintained under 12 h light (30°C, 37% relative humidity)/12 h dark (22°C) cycles. Photon flux density at leaf level was 425 mmol m<sup>-2</sup> s<sup>-1</sup>. Irrigation was withheld on day 1 and recommenced on day 14. Leaves were harvested when plants were well-watered as well as after 4, 9, and 12 days of water deprivation and watered for two days following the drought period.
\ No newline at end of file

assays/Talinum_RNASeq_minimal/protocols/02_RNAex_libraries.md

+```
+Note: 
+- This is a somewhat polished protocol as found in a publication. 
+- This is not an example for a typical lab protocol or method. 
+```
+
+
 # RNA Extraction, Preparation, and Sequencing of Illumina Libraries
 
-The topmost mature unshaded leaves (of approximately 3–4.5 cm length) of T. triangulare were harvested in the middle of the light or the middle of the dark period and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) and quantified with a Qubit 2.0 (Invitrogen). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSEquation 2000 platform, yielding ;14 million reads per library.
+The topmost mature unshaded leaves (of approximately 3–4.5 cm length) of *T. triangulare* were harvested in the middle of the light or the middle of the dark period and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) and quantified with a Qubit 2.0 (Invitrogen). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform.