From fe704c2ce576b3d2a1da844d4dffcb9f23a01a67 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Wed, 5 Feb 2025 13:34:12 +0100
Subject: [PATCH] add arc summary automated by ARCSummary tool

---
 README.md | 168 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 168 insertions(+)

diff --git a/README.md b/README.md
index 3e8bc08..70f7be4 100644
--- a/README.md
+++ b/README.md
@@ -7,3 +7,171 @@
 - 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
+
+
+<!--- Start of automated section -->
+
+# Facultative CAM in Talinum triangulare
+### Description
+Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
+
+<<Test ARC registry>>
+ ## Relationships between Assays and Studies 
+ 
+```mermaid
+---
+title: Facultative-CAM-in-Talinum
+---
+graph TB
+TalinumGenomeDraft_study["TalinumGenomeDraft"];
+TalinumFacultativeCAM_study["TalinumFacultativeCAM"];
+MassHunter_targets_assay["MassHunter_targets"];
+Talinum_RNASeq_minimal_assay["Talinum_RNASeq_minimal"];
+GCqTOF_targets_assay["GCqTOF_targets"];
+TalinumFacultativeCAM_study --> Talinum_RNASeq_minimal_assay;
+TalinumFacultativeCAM_study --> GCqTOF_targets_assay ;
+GCqTOF_targets_assay --> MassHunter_targets_assay 
+class TalinumGenomeDraft_study,TalinumFacultativeCAM_study study;
+class MassHunter_targets_assay,Talinum_RNASeq_minimal_assay,GCqTOF_targets_assay assay;
+classDef assay fill:#4FB3D9,stroke:#333,stroke-width:2px,color:#3A3A3A;
+classDef study fill:#B4CE82,stroke:#333,stroke-width:2px,color:#3A3A3A;
+```
+ 
+_Figure 1:This flowchart highlights the relationship between assays (highlighted in blue) and studies (highlighted in green)_
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Submission Date | July 07, 2015 |
+| Public Release Date | Nov 05, 2015 |
+| Study identifiers | TalinumGenomeDraft , TalinumFacultativeCAM |
+| Study Count | 2 |
+| Assay identifiers | MassHunter_targets , Talinum_RNASeq_minimal , GCqTOF_targets |
+| Assay Count | 3 |
+
+## Table of Contents 
+
+1. [Contacts](#contacts)
+
+ 2. [Publication](#publication)
+
+ 3. Studies 
+
+     - [TalinumGenomeDraft](#study--talinumgenomedraft)
+     - [TalinumFacultativeCAM](#study--talinumfacultativecam)
+ 4. Assays 
+
+     - [MassHunter_targets](#assay--masshunter_targets)
+     - [Talinum_RNASeq_minimal](#assay--talinum_rnaseq_minimal)
+     - [GCqTOF_targets](#assay--gcqtof_targets)
+ 5. [References](#references)
+
+## Contacts 
+ 
+| Names | Email | Address | Affiliation | ORCID |
+| ----- | ----- | ------- | ----------- | ----- |
+| Dominik  Brilhaus | brilhaus@hhu.de | HHU Düsseldorf, 22.07.U1.43, Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0001-9021-3197 | 
+ | Andrea  Bräutigam | andrea.brauetigam@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0002-5309-0527 | 
+ | Tabea  Mettler-Altmann | tabea.mettler@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0002-9161-4889 | 
+ | Klaus  Winter | winterk@si.edu | Balboa, Ancón, Republic of Panama | Smithsonian Tropical Research Institute, Panama |  | 
+ | Andreas P M Weber | aweber@hhu.de | Universitätsstr. 1, 40225 Düsseldorf | Institute of Plant Biochemistry, HHU Düsseldorf | http://orcid.org/0000-0003-0970-4672 |
+
+## Publication 
+
+| Meta Data | Description |
+| ----------- | ----------- |
+| Title | Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare. |
+| Authors | Brilhaus, Dominik; Bräutigam, Andrea; Mettler-Altmann, Tabea; Winter, Klaus; Weber, Andreas P M |
+| PubMedID | 26530316 |
+| DOI | 10.1104/pp.15.01076 |
+| Current status | Published |
+
+## Study : _TalinumGenomeDraft_
+### Description
+ tba 
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Table Count | 1 |
+| Table Names | TalinumGenomeDraft |
+| Sample Count | 1 |
+| Data File Count | 1 |
+| Associated assays |  |
+| Biological replicates | 0 |
+### Annotation headers
+
+## Study : _TalinumFacultativeCAM_
+### Description
+ tba 
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Table Count | 1 |
+| Table Names | plant_material |
+| Sample Count | 6 |
+| Data File Count | 0 |
+| Associated assays | Talinum_RNASeq_minimal , GCqTOF_targets |
+| Biological replicates | 0 |
+### Annotation headers
+
+**Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[organism part](https://bioregistry.io/EFO:0000635),[plant age](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000033)
+
+**Parameters**: [growth day length](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000041),[light intensity exposure](https://bioregistry.io/PECO:0007224),[humidity day](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000005),[temperature day](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000007),[temperature night](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000008)
+
+**Factors**: [watering exposure](https://bioregistry.io/PECO:0007383),[Timepoint](https://bioregistry.io/NCIT:C68568),`timepoint-ZT`,`Photosynthesis mode`
+
+## Assay : _MassHunter_targets_
+### Description
+Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
+
+<<Test ARC registry>>
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Table Count | 2 |
+| Table Names | mh-quant-results , mh-quant-report |
+| Sample Count | 20 |
+| Data File Count | 21 |
+| Associated studies |  |
+### Annotation headers
+
+## Assay : _Talinum_RNASeq_minimal_
+### Description
+Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
+
+<<Test ARC registry>>
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Measurement Type | mRNA Sequencing |
+| Technology Type | Next Generation Sequencing |
+| Table Count | 2 |
+| Table Names | rna_extraction , illumina |
+| Sample Count | 6 |
+| Data File Count | 6 |
+| Associated studies | TalinumFacultativeCAM |
+### Annotation headers
+
+**Parameters**: [biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[extraction method](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000054),[extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[RNA quality check](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000062),[library strategy](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000035),[library selection](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000036),[library layout](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000015),[library preparation kit](http://purl.obolibrary.org/obo/GENEPIO_0000085),[library preparation kit version](http://purl.obolibrary.org/obo/GENEPIO_0000149),[adapter sequence](http://purl.obolibrary.org/obo/GENEPIO_0000083),[next generation sequencing instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000040),[base-calling software](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000017),[base-calling software version](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000018),[Raw data file format](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000021)
+
+## Assay : _GCqTOF_targets_
+### Description
+Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM.
+
+<<Test ARC registry>>
+### Additional details
+| Meta Data | Description |
+| --------- | ----------- |
+| Measurement Type | GCqTOF targeted |
+| Table Count | 3 |
+| Table Names | metabolite_extraction , gas_chromatography , mass_spec |
+| Sample Count | 20 |
+| Data File Count | 20 |
+| Associated studies | TalinumFacultativeCAM |
+### Annotation headers
+
+**Parameters**: [Bio entity](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000012),[Biosource amount](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000013),[Biosource material state](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010009),[Extraction buffer](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000050),[Extraction buffer volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000051),[Internal standard](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010012),[Sample volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010013),[MS sample post-extraction](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000043),[MS sample resuspension](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000044),[MS derivatization](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000052),[MS sample type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000045),[Chromatography instrument model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000046),[Chromatography autosampler model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000047),[Chromatography column type](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000053),[Chromatography column model](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000048),[mobile phase](http://purl.obolibrary.org/obo/CHMO_0000995),[Chromatography injection volume](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010014),[Chromatography injection mode](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0010015),[Chromatography gradient](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000081),[scan polarity](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000465),[scan window lower limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501),[scan window upper limit](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000500),[scan rate](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000015),[instrument model](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031),[ionization type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000008),[mass analyzer type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000443),[detector type](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000026)
+
+## References 
+ _add your references here_
+
+<!--- End of automated section -->
\ No newline at end of file
-- 
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