Replace mermaid with auto-generated-from-ISA version

README.md

@@ -26,148 +26,129 @@ Any additional information required to reanalyze the data reported in this paper
 ## ARC structure
 
 ``` mermaid
-%%{
-  init: {
-    'theme': 'base',
-    'themeVariables': {
-      'background': '#fff',
-      'lineColor': '#2d3e50',
-      'primaryTextColor': '#2d3e50'
-    }
-  }
-}%%
-
 flowchart
 
-subgraph Legend
-l1(Sample)
-l2>Process]
-l3(Material)
-l4(Data)
+subgraph CarbohydrateSubstratesForImmunityAndEnzymaticDigestionAssays
+end
+
+subgraph HordeumVulgare
+  ROS_burst_assay_preparation
+  germination
+  growth_chamber
 end
 
-subgraph studies\NicotianaBenthamiana
-direction TB
-s1(wild type seeds)---p1>PlantMaterialAndGrowthConditions.md]-->s2(N. benthamiana plants)
+subgraph NicotianaBenthamiana
+  greenhouse_conditions
 end
 
-subgraph studies\HordeumVulgare
-direction TB
-s3(barley seeds)---p2>PlantMaterialAndGrowthConditions.md]-->s4(barley plants)
+subgraph HeterologousProteinProductionAndPurification
+  Agrobacterium_growth
+  Nicotiana_infiltration
+  ground_material
+  incubation
+  purification
 end
 
-subgraph studies\CarbohydrateSubstratesForImmunityAndEnzymaticDigestionAssays
-direction TB
-p3>CarbohydrateSubstratesForImmunityAndEnzymaticDigestionAssays.md]-->s5(carbohydrate substrates)
+subgraph PlasmidConstructionForHeterologousProteinProduction
+  amplification
+  cloning
+  site-directed_mutagenesis_PCR
+  purification_and_E.coli_transfo
+  Agrobacterium_transformation
 end
 
-subgraph assays\HeterologousProteinProductionAndPurification
-direction TB
-a1(codon-optimized GBP1 sequence)---p4>PlasmidConstruction.md]-->a2(pXCScpmv-GBP1-HAStrep)
-a3(catalitically inactive GBP1 sequence)---p4-->a4(pXCScpmv-GBP1_E500A-HAStrep)
-a2----p6>"`isolation
-        sequencing
-        _Agrobacterium tumefaciens_ transformation`"]
-a4---p5>"`gel electrophoresis
-        purification
-        _E.coli_ transformation`"]---p6
-p6-->a5(Agrobacterium_GBP1)
-p6-->a6(Agrobacterium_GBP1_E500A)
-a5 & a6---p7>infiltration]
-s2----p7
-p7---p8>HeterologousProteinProductionAndPurification.md]-->a7(purified proteins)
+subgraph ProteinPull-down
+  biothinylation_of_laminarin
+  extraction
+  incubation
+  pull-down
+  SDS-PAGE
 end
 
-subgraph assays\EnzymaticCarbohydrateDigestionAndTLC
-direction TB
-a7 & s5---p9>EnzymaticCarbohydrateDigestion.md]-->a8(digestion products)
-a8---p10>TLC.md]-->d1("`gr3b_lrg.jpg
-                    gr4a_lrg.jpg
-                    gr4b_lrg.jpg
-                    gr4c_lrg.jpg
-                    FigS4A.jpg
-                    FigS4B.jpg
-                    FigS5A.png`")
+subgraph OxidativeBurstAssay
+  preparation_of_plant_material
+  ROS_burst_assay
 end
 
-subgraph assays\MALDI-TOFAnalysis
-direction TB
-a8---p11>MALDI-TOFAnalysis.md]-->d2("`gr3c_large.jpg
-FigS4C.jpg`")
+subgraph MALDI-TOFAnalysis
+  MALDI-TOF
 end
 
-subgraph assays\CRISPRCas9-basedMutagenesis
-direction TB
-s4---p12>CRISPRCas9-basedMutagenesis.md]-->a9(barley mutants)-->d15(gr1b_lrg.jpg)
+subgraph EnzymaticCarbohydrateDigestionAndTLC
+  EnzymaticCarbohydrateDigestion
+  TLC
 end
 
-subgraph assays\OxidativeBurstAssay
-direction TB
-s2 & s4 & a9---p13>PreparationOfThePlantMaterial.md]-->a10(plant material)
-a10---p14>ROSBurstAssay.md]-->d3("`gr5_lrg.jpg
-                                FigS1A.jpg
-                                FigS1B.jpg
-                                FigS5B.jpg
-                                FigS5C.jpg`")
+subgraph StainingForConfocalMicroscopy
+  staining
 end
 
-subgraph assays\FungalMaterialGrowthConditionsAndBarleyColonizationAssays
-direction TB
-s4 & a9---p15>RhizophagusIrregularis.md]-->a11(R. irregularis colonized plants)-->d11(FigS3B.jpg)
-s4 & a9---p16>BlumeriaHordei.md]-->a12(B. hordei colonized plants)-->d13(FigS3D.jpg)
-s4 & a9---p17>SerendipitaIndicaSerendipitaVermiferaAndBipolarisSorokiniana.md]-->a13(S. indica colonized plants) & a14(S. vermifera colonized plants) & a15(B. sorokiniana colonized plants)
-a15-->d12(FigS3C.jpg)
-d14(gr6b_lrg.jpg)
+subgraph CRISPRCas9-basedMutagenesis
+  expression_cassettes
+  plasmid_generation
+  CRISPR_Cas9_mutagenesis
 end
 
-subgraph assays\qRT-PCR
-direction TB
-a12 & a13 & a14 & a15---p18>qRT-PCR.md]-->d4("`gr1c_lrg.jpg
-gr2_lrg.jpg
-gr6d_lrg.jpg`")
+subgraph MultipleSequenceAlignment
+  alignment
 end
 
-subgraph assays\StainingForConfocalMicroscopy
-direction TB
-a13---p19>HordeumVulgare.md]-->d5("`gr6a_lrg.jpg
-                                FigS6A.jpg
-                                FigS6B.jpg
-                                FigS6C.jpg`")
-a11---p20>RootStainingOfRIrregularis.md]-->d6(FigS3A.jpg)
+subgraph MS-MSAnalysisOfThePull-downProteins
+  MS-MS_analysis
 end
 
-subgraph assays\ProteinPull-down
-direction TB
-a16(laminarin)---p21>BiotinylationOfLaminarin.md]-->a17(biotinylated laminarin)
-s4 & a17---p22>ProteinPull-downWithBiotinylatedLaminarin.md]-->a18(pull-down proteins)
-a18---p23>SDS-PAGE separation]-->d7(FigS1C.jpg)
+subgraph FungalMaterialGrowthConditionsAndBarleyColonizationAssays
+  R.irregularis
+  R.irregularis_staining
+  Si_Sv_Bs
+  B.hordei
+  B.hordei_staining
 end
 
-subgraph assays\MS-MSAnalysisOfThePull-downProteins
-direction TB
-a18---p24>MS-MSAnalysisOfThePull-downProteins.md]-->d8("`gr1a_lrg.jpg
-         mmc2.xlsx`")
+subgraph QuantificationAndStatisticalAnalyses
 end
 
-subgraph assays\MultipleSequenceAlignment
-d9(gr4a_lrg.jpg)
+subgraph qRT-PCR
+  RT-PCR
 end
 
-subgraph assays\QuantificationAndStatisticalAnalysis
-direction TB
-pr25>QuantificationAndStatisticalAnalysis.md]-->d10("`gr6c_lrg.jpg
-        mmc3.xlsx`")
-end
-
-%% Defining node styles
-  classDef S fill:#b4ce82, stroke:#333;
-  classDef M fill:#ffc000;
-  classDef D fill:#c21f3a,color:white;
-  classDef P stroke-width:0px; 
-
-%% Assigning styles to nodes
-    class l1,a7,a8,a18 S;
-    class l3,s1,s2,s3,s4,s5,a1,a2,a3,a4,a5,a6,a9,a10,a11,a12,a13,a14,a15,a16,a17 M;
-    class d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,l4 D;
-    class l2,p1,p2,p3,p4,p5,p6,p7,p8,p9,p10,p11,p12,p13,p14,p15,p16,p17,p18,p19,p20,p21,p22,p23,p24,p25 P;
+
+Wanke-2023 --> CarbohydrateSubstratesForImmunityAndEnzymaticDigestionAssays
+Wanke-2023 --> HordeumVulgare
+Wanke-2023 --> NicotianaBenthamiana
+
+ROS_burst_assay_preparation --3--> germination
+germination --3--> growth_chamber
+growth_chamber --3--> preparation_of_plant_material
+growth_chamber --1--> R.irregularis
+growth_chamber --1--> Si_Sv_Bs
+growth_chamber --1--> B.hordei
+greenhouse_conditions --1--> preparation_of_plant_material
+Agrobacterium_growth --3--> Nicotiana_infiltration
+Nicotiana_infiltration --1--> ground_material
+ground_material --1--> incubation
+incubation --1--> purification
+purification --2--> EnzymaticCarbohydrateDigestion
+amplification --1--> cloning
+cloning --1--> site-directed_mutagenesis_PCR
+cloning --1--> Agrobacterium_transformation
+site-directed_mutagenesis_PCR --1--> purification_and_E.coli_transfo
+purification_and_E.coli_transfo --1--> Agrobacterium_transformation
+Agrobacterium_transformation --2--> Agrobacterium_growth
+biothinylation_of_laminarin --1--> extraction
+extraction --1--> incubation
+incubation --6--> pull-down
+pull-down --6--> SDS-PAGE
+SDS-PAGE --5--> MS-MS_analysis
+preparation_of_plant_material --6--> ROS_burst_assay
+EnzymaticCarbohydrateDigestion --28--> MALDI-TOF
+EnzymaticCarbohydrateDigestion --28--> TLC
+expression_cassettes --3--> plasmid_generation
+plasmid_generation --1--> CRISPR_Cas9_mutagenesis
+CRISPR_Cas9_mutagenesis --2--> ROS_burst_assay_preparation
+R.irregularis --3--> R.irregularis_staining
+Si_Sv_Bs --3--> staining
+Si_Sv_Bs --9--> RT-PCR
+B.hordei --3--> B.hordei_staining
+```