diff --git a/README.md b/README.md index 0386d382e0b328aa4a7571332fc70aa1bd894845..e06ab24533adb396c8b3487884cf9904dec0e4fe 100644 --- a/README.md +++ b/README.md @@ -14,4 +14,97 @@ This is an Open Access article distributed under the terms of the Creative Commo ## Data availability -The read data as well as processed files are deposited at the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE116590 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116590). \ No newline at end of file +The read data as well as processed files are deposited at the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE116590 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116590). + +## ARC Overview + +```mermaid +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["Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare"] + class id_0 investigationStyle; + id_0-->STUDY_id_1 + class STUDY_id_1 studyStyle; + subgraph STUDY_id_1[Study: Maleckova2018_aba] + id_2[plant_material] + class id_2 processStyle; + id_3[treatment_harvest] + class id_3 processStyle; + end + subgraph ASSAY_id_4[Assay: TitratableAcidity] + id_5[SamplePreparation] + class id_5 processStyle; + id_6[AcidityMeasurement] + class id_6 processStyle; + end + class ASSAY_id_4 assayStyle; + subgraph ASSAY_id_7[Assay: ProteinAndStarchMeasurements] + id_8[SamplePrep-Protein] + class id_8 processStyle; + id_9[ProteinMeasurement] + class id_9 processStyle; + id_10[PelletGelatinization] + class id_10 processStyle; + id_11[OvernightDigest] + class id_11 processStyle; + id_12[BufferPreparation] + class id_12 processStyle; + id_13[StarchMeasurement] + class id_13 processStyle; + end + class ASSAY_id_7 assayStyle; + subgraph ASSAY_id_14[Assay: CMML_18-0008_LCqTOF] + id_15[metabolite_extraction-lc] + class id_15 processStyle; + id_16[liquid_chromatography] + class id_16 processStyle; + end + class ASSAY_id_14 assayStyle; + subgraph ASSAY_id_17[Assay: CMML_18-0008_GC-MS] + id_18[metabolite_extraction-gc] + class id_18 processStyle; + id_19[gas_chromatography] + class id_19 processStyle; + id_20[mass_spectrometry] + class id_20 processStyle; + end + class ASSAY_id_17 assayStyle; + subgraph ASSAY_id_21[Assay: Maleckova2018_aba_mRNASeq] + id_22[RNAex] + class id_22 processStyle; + id_23[Illumina] + class id_23 processStyle; + end + class ASSAY_id_21 assayStyle; + subgraph ASSAY_id_24[Assay: CMML_18-0008_LCqTOF-MasshunterQuant] + end + class ASSAY_id_24 assayStyle; + subgraph ASSAY_id_25[Assay: CMML_18-0008_GC-MS-MasshunterQuant] + end + class ASSAY_id_25 assayStyle; + subgraph ASSAY_id_26[Assay: CMML_18-0008_HPLC-DAD] + end + class ASSAY_id_26 assayStyle; + id_2-->|24|id_3 + id_3-->|24|id_5 + id_3-->|24|id_8 + id_3-->|24|id_15 + id_3-->|24|id_18 + id_3-->|24|id_22 + id_5-->|24|id_6 + id_5-->|24|id_9 + id_8-->|24|id_6 + id_8-->|24|id_9 + id_8-->|24|id_10 + id_10-->|24|id_11 + id_11-->|24|id_13 + id_12-->|1|id_13 + id_15-->|48|id_16 + id_18-->|48|id_19 + id_19-->|63|id_20 + id_22-->|24|id_23 + +``` diff --git a/arc-mermaid.md b/arc-mermaid.md deleted file mode 100644 index d21098cb0bf46391551de9a20ecddeb65688a236..0000000000000000000000000000000000000000 --- a/arc-mermaid.md +++ /dev/null @@ -1,45 +0,0 @@ -```mermaid -flowchart TD - Maleckova-2019-Talinum-ABA[Maleckova-2019-Talinum-ABA] - Maleckova-2019-Talinum-ABA-->STUDY_Maleckova2018_aba - subgraph STUDY_Maleckova2018_aba[Study:Maleckova2018_aba] - plant_material[plant_material] - treatment_harvest[treatment_harvest] - end - subgraph ASSAY_CMML_18-0008_LCqTOF[Assay:CMML_18-0008_LCqTOF] - metabolite_extraction[metabolite_extraction] - liquid_chromatography[liquid_chromatography] - end - subgraph ASSAY_CMML_18-0008_GC-MS[Assay:CMML_18-0008_GC-MS] - metabolite_extraction[metabolite_extraction] - gas_chromatography[gas_chromatography] - mass_spectrometry[mass_spectrometry] - end - subgraph ASSAY_Maleckova2018_aba_mRNASeq[Assay:Maleckova2018_aba_mRNASeq] - RNAex[RNAex] - Illumina[Illumina] - end - subgraph ASSAY_CMML_18-0008_LCqTOF-MasshunterQuant[Assay:CMML_18-0008_LCqTOF-MasshunterQuant] - end - subgraph ASSAY_CMML_18-0008_GC-MS-MasshunterQuant[Assay:CMML_18-0008_GC-MS-MasshunterQuant] - end - subgraph ASSAY_CMML_18-0008_HPLC-DAD[Assay:CMML_18-0008_HPLC-DAD] - end - plant_material-->|24|treatment_harvest - treatment_harvest-->|24|metabolite_extraction - treatment_harvest-->|24|metabolite_extraction_1 - treatment_harvest-->|24|RNAex - metabolite_extraction-->|48|liquid_chromatography - metabolite_extraction_1-->|48|gas_chromatography - gas_chromatography-->|63|mass_spectrometry - RNAex-->|24|Illumina - -classDef inv fill:#6c7885,color:#2d3e50,font-weight:bold; -classDef study fill:#62d4c1,color:#2d3e50,font-weight:bold; -classDef assay fill:#ffd34d,color:#2d3e50,font-weight:bold; -classDef process fill:#D46275,color:#2d3e50,font-weight:; -class Maleckova-2019-Talinum-ABA inv; -class STUDY_Maleckova2018_aba study; -class ASSAY_CMML_18-0008_LCqTOF,ASSAY_CMML_18-0008_GC-MS,ASSAY_Maleckova2018_aba_mRNASeq,ASSAY_CMML_18-0008_LCqTOF-MasshunterQuant,ASSAY_CMML_18-0008_GC-MS-MasshunterQuant,ASSAY_CMML_18-0008_HPLC-DAD assay; -class plant_material,treatment_harvest,metabolite_extraction,liquid_chromatography,metabolite_extraction_1,gas_chromatography,mass_spectrometry,RNAex,Illumina process; -```