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Commit 8d8cf519 authored by Viktoria Petrova's avatar Viktoria Petrova
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update README with new mermaid graph

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......@@ -14,32 +14,15 @@ High ambient temperature (HT) impairs reproductive development and grain yield i
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
## Table of Contents
1. Studies
- [plant-samples](#study--plant-samples)
2. Assays
- [Salmon_quantification](#assay--salmon_quantification)
- [RNAseq_raw_data](#assay--rnaseq_raw_data)
- [FASTQC](#assay--fastqc)
## Relationships between Assays and Studies
### Relationships between Assays and Studies
```mermaid
---
title: Effects_of_Ppd-H1_and_High_Ambient_Temperatures_in_Barley
---
flowchart TD
classDef investigationStyle fill:#6c7885,color:#2d3e50,fontWeight:bold;
classDef studyStyle fill:#62d4c1,color:#2d3e50,fontWeight:bold;
classDef assayStyle fill:#ffd34d,color:#2d3e50,fontWeight:bold;
classDef processStyle fill:#D46275,color:#2d3e50;
id_0["PPD-H1Improves Stress Resistance and Energy Metabolism to Boost Spike Fertility under High Ambient Temperatures"]
id_0["PHOTOPERIOD 1 enhances stress tolerance and energy metabolism to promote spike fertility in barley under high ambient temperatures"]
class id_0 investigationStyle;
id_0-->STUDY_id_1
class STUDY_id_1 studyStyle;
......@@ -47,114 +30,33 @@ flowchart TD
id_2[plant-characteristics]
class id_2 processStyle;
end
subgraph ASSAY_id_3[Assay: Salmon_quantification]
id_4[salmon]
subgraph ASSAY_id_3[Assay: FASTQC]
id_4[FastQC]
class id_4 processStyle;
end
class ASSAY_id_3 assayStyle;
subgraph ASSAY_id_5[Assay: RNAseq_analysis_of_MSA]
subgraph ASSAY_id_5[Assay: RNAseq_raw_data]
id_6[illumina]
class id_6 processStyle;
end
class ASSAY_id_5 assayStyle;
subgraph ASSAY_id_6[Assay: RNAseq_raw_data]
id_7[illumina]
class id_7 processStyle;
end
class ASSAY_id_6 assayStyle;
subgraph ASSAY_id_8[Assay: RNAseq_analysis_of_leaf]
subgraph ASSAY_id_7[Assay: Salmon_quantification]
id_8[salmon]
class id_8 processStyle;
end
class ASSAY_id_8 assayStyle;
subgraph ASSAY_id_9[Assay: FASTQC]
id_4[salmon]
class id_4 processStyle;
class ASSAY_id_7 assayStyle;
subgraph ASSAY_id_9[Assay: ThreeDRNAseq]
id_10[TPM_leaf]
class id_10 processStyle;
id_11[CPM_leaf]
class id_11 processStyle;
end
class ASSAY_id_9 assayStyle;
id_2-->|188|id_7
id_7-->|382|id_4
```
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Submission Date | tba |
| Public Release Date | tba |
| Study identifiers | plant-samples |
| Study Count | 1 |
| Assay identifiers | Salmon_quantification , RNAseq_analysis_of_MSA , RNAseq_raw_data , RNAseq_analysis_of_leaf , FASTQC |
| Assay Count | 5 |
id_2-->|188|id_6
id_4-->|1|id_4
id_6-->|382|id_4
id_6-->|382|id_8
id_8-->|84|id_10
id_8-->|84|id_11
## Contacts
| Names | Email | Address | Affiliation | ORCID |
| ----- | ----- | ------- | ----------- | ----- |
| Tianyu Lan | tianyu.lan@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Agatha Walla | Walla@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
| Kumsal Ecem Çolpan Karışan | kumsal.colpan@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
| Gabriele Buchmann | gabriele.buchmann@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Vera Wewer | vwewer@uni-koeln.de | | CEPLAS Plant Metabolism and Metabolomics Facility, Institute for Plant Sciences, University of Cologne, 50674 Cologne, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
| Sabine Metzger | s.metzgar@uni-koeln.de | | CEPLAS Plant Metabolism and Metabolomics Facility, Institute for Plant Sciences, University of Cologne, 50674 Cologne, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
| Isaia Vardanega | isaia.vardanega@hhu.de | | Institute of Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Einar Baldvin Haraldsson | einar.haraldsson@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Gesa Helmsorig | gesa.helmsorig@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Venkatasubbu Thirulogachandar | thirulogachandar.venkatasubbu@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany | |
| Rüdiger Simon | ruediger.simon@hhu.de | | Institute of Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
| Maria von Korff | maria.korff.schmissing@hhu.de | | Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, 40225 Düsseldorf, Germany | |
## Study: _plant-samples_
### Description
tba
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Table Count | 1 |
| Table Names | plant-characteristics |
| Sample Count | 188 |
| Data File Count | 0 |
| Associated assays | RNAseq_raw_data |
| Biological replicates | 0 |
### Annotation headers
**Characteristics**: [organism](https://bioregistry.io/OBI:0100026),[genotype](https://bioregistry.io/EFO:0000513),[biological replicate](https://bioregistry.io/EFO:0002091),[plant structure](https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPO_0009011)
**Factors**: `temperature treatment`,`waddington stage`
## Assay: _Salmon_quantification_
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Table Count | 1 |
| Table Names | NewTable0 |
| Sample Count | 388 |
| Data File Count | 388 |
| Associated studies | |
### Annotation headers
## Assay: _RNAseq_raw_data_
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Measurement Type | RNA-Seq |
| Technology Type | Illumina NovaSeq 6000 |
| Table Count | 1 |
| Table Names | illumina |
| Sample Count | 388 |
| Data File Count | 388 |
| Associated studies | plant-samples |
### Annotation headers
**Parameters**: [library strategy](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000035),[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),[base-calling software parameters](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000019),[Raw data file format](http://purl.org/nfdi4plants/ontology/dpbo/DPBO_0000021)
## Assay: _FASTQC_
### Additional details
| Meta Data | Description |
| --------- | ----------- |
| Technology Type | FASTQC |
| Table Count | 1 |
| Table Names | NewTable0 |
| Sample Count | 840 |
| Data File Count | 0 |
| Associated studies | |
### Annotation headers
**Characteristics**: [Format](https://bioregistry.io/NCIT:C42761)
```
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