##PROJECT																																																		
Project Identifier	Project Title*	Project Type	Project Summary	Institute*	Department*	Laboratory	Funding source	Principal Investigator Last Name*	Principal Investigator First Name*	Address	Email*	Phone																																						
Project ID (will be added)	Rice Infection Project	Metabolomic and transcriptomic analysis	Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae	UC Davis	Davis Genome Center	Fiehn		Fiehn	Oliver	"451 E. Health Sci. Drive, Davis, California 95616, USA"	ofiehn@ucdavis.edu																																							
##ENDPROJECT																																																		
##STUDY																																																		
Study Identifier	Study Title*	"Study type* (timecourse,drug dosage,etc.)"	Study Summary (Description/Design)*	Institute*	Department*	Laboratory	Study contact person: Last Name*	Study contact person: First Name*	Address	Email*	Phone	Submission Date (MM-DD-YYYY)*	Number of Groups*	Total Number of subjects/patients/samples*	Study Comments																																			
Study ID (will be added)	Rice Infection Study	MS analysis	"Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), gives rise to devastating crop losses in rice. Disease resistant rice cultivars are the most economical way to combat the disease. The TP309 cultivar is susceptible to infection by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern recognition receptor Xa21, and is resistant. PXO99?raxST, a strain lacking the raxST gene, is able to overcome Xa21-mediated immunity. We used a single extraction solvent to demonstrate comprehensive metabolomics and transcriptomics profiling under sample limited conditions, and analyze the molecular responses of two rice lines challenged with either PXO99 or PXO99?raxST. LCTOF raw data file filtering resulted in better within group reproducibility of replicate samples for statistical analyses. Accurate mass match compound identification with molecular formula generation (MFG) ranking of 355 masses was achieved with the METLIN database. GCTOF analysis yielded an additional 441 compounds after BinBase database processing, of which 154 were structurally identified by retention index/MS library matching. Multivariate statistics revealed that the susceptible and resistant genotypes possess distinct profiles. Although few mRNA and metabolite differences were detected in PXO99 challenged TP309 compared to mock, many differential changes occurred in the Xa21-mediated response to PXO99 and PXO99?raxST. Acetophenone, xanthophylls, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic pathways were affected. Significant transcriptional induction of several pathogenesis related genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, ICL1 and Glutathione-S-transferase transcripts indicated limited correlation with metabolite changes under single time point global profiling conditions."	UC Davis	Davis Genome Center	Fiehn	Kind	Tobias	"451 E. Health Sci. Drive, Davis, California 95616, USA"	tkind@ucdavis.edu		02-22-2013	7	60																																				
##ENDSTUDY																																																		
##SUBJECT_FACTOR																																																		
Sample Identifier	Factor1	Factor2																																																
Local Sample ID	genotype	Xoo infection																																																
20526	Taipei 309 +Xa21 transgene	no treatment																																																
20536	Taipei 309 +Xa21 transgene	no treatment																																																
20551	Taipei 309 +Xa21 transgene	no treatment																																																
20561	Taipei 309 +Xa21 transgene	no treatment																																																
20541	Taipei 309 +Xa21 transgene	no treatment																																																
20566	Taipei 309 +Xa21 transgene	no treatment																																																
20531	Taipei 309 +Xa21 transgene	no treatment																																																
20546	Taipei 309 +Xa21 transgene	no treatment																																																
20556	Taipei 309 +Xa21 transgene	no treatment																																																
20204	Taipei 309 +Xa21 transgene	Pxo99																																																
20306	Taipei 309 +Xa21 transgene	Pxo99																																																
20296	Taipei 309 +Xa21 transgene	Pxo99																																																
20209	Taipei 309 +Xa21 transgene	Pxo99																																																
20184	Taipei 309 +Xa21 transgene	Pxo99																																																
20199	Taipei 309 +Xa21 transgene	Pxo99																																																
20301	Taipei 309 +Xa21 transgene	Pxo99																																																
20189	Taipei 309 +Xa21 transgene	Pxo99																																																
20194	Taipei 309 +Xa21 transgene	Pxo99																																																
20505	Taipei 309	no treatment																																																
20510	Taipei 309	no treatment																																																
20500	Taipei 309	no treatment																																																
20485	Taipei 309	no treatment																																																
20480	Taipei 309	no treatment																																																
20495	Taipei 309	no treatment																																																
20490	Taipei 309	no treatment																																																
20515	Taipei 309	no treatment																																																
20520	Taipei 309	no treatment																																																
20434	Taipei 309 +Xa21 transgene	mock																																																
20439	Taipei 309 +Xa21 transgene	mock																																																
20449	Taipei 309 +Xa21 transgene	mock																																																
20459	Taipei 309 +Xa21 transgene	mock																																																
20444	Taipei 309 +Xa21 transgene	mock																																																
20454	Taipei 309 +Xa21 transgene	mock																																																
20153	Taipei 309	Pxo99																																																
20173	Taipei 309	Pxo99																																																
20286	Taipei 309	Pxo99																																																
20281	Taipei 309	Pxo99																																																
20163	Taipei 309	Pxo99																																																
20168	Taipei 309	Pxo99																																																
20291	Taipei 309	Pxo99																																																
20178	Taipei 309	Pxo99																																																
20158	Taipei 309	Pxo99																																																
20372	Taipei 309 +Xa21 transgene	RaxSt																																																
20367	Taipei 309 +Xa21 transgene	RaxSt																																																
20357	Taipei 309 +Xa21 transgene	RaxSt																																																
20382	Taipei 309 +Xa21 transgene	RaxSt																																																
20352	Taipei 309 +Xa21 transgene	RaxSt																																																
20362	Taipei 309 +Xa21 transgene	RaxSt																																																
20377	Taipei 309 +Xa21 transgene	RaxSt																																																
20342	Taipei 309 +Xa21 transgene	RaxSt																																																
20347	Taipei 309 +Xa21 transgene	RaxSt																																																
20418	Taipei 309	mock																																																
20388	Taipei 309	mock																																																
20423	Taipei 309	mock																																																
20403	Taipei 309	mock																																																
20428	Taipei 309	mock																																																
20408	Taipei 309	mock																																																
20413	Taipei 309	mock																																																
20398	Taipei 309	mock																																																
20393	Taipei 309	mock																																																
##ENDSUBJECT_FACTOR																																																		
##SUBJECT																																																		
Subject Identifier	"Subject Type (Human, Aminal, Plant, Cells)*"	Subject Species*	Taxonomy ID	Genotype/Strain	Age or Age Range	Weight or Weight range	Height or Height range	Gender	HUMAN:Race	HUMAN:Ethnicity	HUMAN:Trial Type	HUMAN:Lifestyle Factors	HUMAN:Medications	HUMAN:Prescription/OTC	HUMAN:Smoking Status	HUMAN:Alcohol/Drug Use	HUMAN:Nutrition	HUMAN:Inclusion Criteria	HUMAN:Exclusion Criteria	ANIMAL:Animal Supplier	ANIMAL:Housing	ANIMAL:Light cycle	ANIMAL:Feed	ANIMAL:Water	ANIMAL:Inclusion Criteria	CELL:Biosource or Supplier	CELL:Strain Details	CELL:Primary or immortalized	CELL:Passage number	CELL:Cell counts	Subject Comments																			
Subject ID (will be added)		 Oryza sativa 	39947	Taipei 309																																														
##ENDSUBJECT		 Oryza sativa 	39947	Taipei 309 +Xa21 transgene																																														
##TREATMENT																																																		
Treatment Type Identifier	Treatment Summary	Treatment Protocol ID	Treatment Protocol Filename	Treatment Protocol Comments	"Treatment (Abiotic, Biotic, Intervention)"	Treatment Compound	Treatment Route	Treatment Dose	Treatment Dose Volume	Treatment Dose Duration	Treatment Vehicle	ANIMAL:Veterinary Treatments	ANIMAL:Anesthesia	ANIMAL:Acclimation Duration	ANIMAL:Fasting	ANIMAL:EndPoints Euthanasia	ANIMAL:EndPoints Tissue Collection List	ANIMAL:EndPoints Tissue Processing Method	ANIMAL:EndPoints Clinical Signs	HUMAN:Fasting	HUMAN:EndPoints Clinical Signs	CELL:Storage	CELL:Growth Container	CELL:Growth Configuration	CELL:Growth Rate	CELL:Percent confluence	CELL:Inoculation Procedure	CELL:Media	CELL:Time since last media change	CELL:Environmental Conditions	CELL:Harvesting	PLANT:Growth Support	PLANT:Growth Location	PLANT:Plot Design	PLANT:Light Period 	PLANT:Humidity	PLANT:Temperature	PLANT:Watering Regime	PLANT:Nutritional Regime	PLANT:Date of Plant Establishment	PLANT:Harvest Date	PLANT:Growth Stage	PLANT:Metabolism Quenching Method 	PLANT:Harvest Method	PLANT:Storage					
Treatment Type ID (will be added)				no treatment																																														
##ENDTREATMENT				Pxo99																																														
##COLLECTION				mock																																														
Collection Identifier	Collection Summary	Collection Protocol ID	Collection Protocol Filename	Collection Protocol Comments	"Sample Type (Blood, Urine, Saliva, Tissue, Cell, other)*"	Collection Method	Collection Location	Collection Frequency	Collection Duration	Time of Collection (Relative to dose)	Volume/Amount Collected	Storage Conditions	Collection Vials	Storage Vials	Collection Tube Temp	Additives	BLOOD Serum or Plasma	TISSUE/CELL Identification	TISSUE/CELL Quantity Taken																															
Collection ID (will be added)																																																		
##ENDCOLLECTION																																																		
##SAMPLEPREP																																																		
Sample Prep Identifier	Sample Prep Summary	Sample Prep Protocol ID	Sample Prep Protocol Filename	Sample Prep Protocol Comments	"Processing Method (Lyophilization, Homogenization, Lysis, etc)"	Processing Storage conditions	Extraction Method	Extract Concentration/Dilution	"Extract Enrichment (SPE, Desalting, etc)"	Extract Cleanup	Extract Storage	Sample Resuspension	Sample Derivatization	"Sample Spiking (Internal Standards, Retention Standards, etc)"	Organ	Organ Specification	Cell Type	Subcellular Location																																
Sample Prep ID (will be added)																																																		
##ENDSAMPLEPREP																																																		
##CHROMATOGRAPHY																																																		
Chromatography Identifier	Chromatography Summary	Methods File ID	Methods Filename	Chromatography Comments	Instrument Name	Column Name	Column Pressure	Column Temperature	Flow Gradient	Flow Rate	Injection Temperature	Internal Standard	Internal Standard MT	Retention Index	Retention Time	Sample Injection	Sampling Cone	Solvent A	Solvent B	Analytical Time	Capillary Voltage	Migration Time	Oven Temperature	Preconditioning	Running Buffer	Running Voltage	Sheath Liquid	Time Program	Transferline Temperature	Washing Buffer	Weak Wash Solvent Name	Weak Wash Volume	Strong Wash Solvent Name	Strong Wash Volume	Target Sample Temperature	Sample Loop Size	Sample Syringe Size	Randomization Order												
Chromatography ID (will be added)																																																		
##ENDCHROMATOGRAPHY																																																		
##ANALYSIS																																																		
Analysis Identifier	Laboratory Name	Operator Name	"Analysis Type (MS, NMR, other)"	Instrument Name	Software/Version	Instrument Parameters File	Analysis Protocol ID	Analysis Comments	Acqusition Date	Acqusition Time	Acquisition ID	Acquisition Parameters File	Acquired (Raw) File	Processing Parameters File	Processed File	Randomization Order	Detector Type	Data Format																																
Analysis ID (will be added)																																																		
##ENDANALYSIS																																																		
##MS																																																		
MS Identifier	Analysis Identifier	Instrument Type	MS Type	MS Comments	Ion Mode	Capillary Temperature	Capillary Voltage	Collision Energy	Collision Gas	Dry Gas Flow	Dry Gas Temp	Fragment Voltage	Fragmentation Method	Gas Pressure	Helium Flow	Ion Source Temperature	Ion Spray Voltage	Ionization	Ionization Energy	Ionization Potential	Mass Accuracy	Precursor Type	Reagent Gas	Source Temperature	Spray Voltage	Activation Parameter	Activation Time	Atom Gun Current	Automatic Gain Control	Bombardment	CDL Side Octopoles Bias Voltage	CDL Temperature	Data Format	Desolvation Gas Flow	Desolvation Temperature	Interface Voltage	IT Side Octopoles Bias Voltage	Laser	Matrix	Nebulizer	Octpole Voltage	Probe Tip	Resolution Setting	Sample Dripping	Scan Range M/Z	Scanning	Scanning Cycle	Scanning Range	Skimmer Voltage	Tube Lens Voltage
MS ID (will be added)	Analysis ID (will be added)																																																	
##ENDMS																																																		
##NMR																																																		
NMR Identifier	Analysis Identifier	Instrument Type	NMR Experiment type	NMR Comments	Field Frequency Lock	Standard Concentration	Spectrometer Frequency	NMR Probe	NMR Solvent	NMR Tube Size	Shimming Method	Pulse Sequence	Water Suppression	Pulse Width	Power Level	Receiver Gain	Offset Frequency (Water Suppression)	Presaturation Power level	Chemical Shift Reference Compound	Temperature	Number of Scans (Transients)	Dummy Scans	Acquisition Time	Relaxation Delay	Spectral Width	Number of Data Points (TD) Acquired	Real Data Points (SI)	Line Broadening	Zero Filling	Apodization	Baseline Correction Method	Chemical Shift Reference Standard	Binned data bin increment (ppm)	Binned data normalization method	Binned data protocol file	Binned data chemical shift range (ppm)	Binned data excluded ranges (ppm)													
NMR ID (will be added)	Analysis ID (will be added)																																																	
##ENDNMR																																																		
