Summary of Study ST000007

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000006. The data can be accessed directly via it's Project DOI: 10.21228/M8CC7R This work is supported by NIH grant, U2C- DK119886.


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Study IDST000007
Study TitleRice Infection Study
Study TypeMS analysis
Study SummaryBacterial 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.
University of California, Davis
DepartmentDavis Genome Center
Last NameKind
First NameTobias
Address451 E. Health Sci. Drive, Davis, California 95616, USA
Submit Date2013-02-22
Num Groups7
Total Subjects60
Raw Data AvailableNo
Analysis Type DetailGC-MS
Release Date2013-03-24
Release Version1
Tobias Kind Tobias Kind application/zip

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Project ID:PR000006
Project DOI:doi: 10.21228/M8CC7R
Project Title:Rice Infection Project
Project Type:Metabolomic and transcriptomic analysis
Project Summary:Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae
Institute:University of California, Davis
Department:Davis Genome Center
Last Name:Fiehn
First Name:Oliver
Address:451 E. Health Sci. Drive, Davis, California 95616, USA


Subject ID:SU000009
Subject Type:Plant
Subject Species:Oryza sativa Japonica Group
Taxonomy ID:39947
Genotype Strain:Taipei 309 +Xa21 transgene | Taipei 309; At1g08510
Species Group:Plant


Subject type: Plant; Subject species: Oryza sativa Japonica Group (Factor headings shown in green)

mb_sample_id local_sample_id genotype Xoo infection
SA00027220434Taipei 309 +Xa21 transgene mock
SA00027320439Taipei 309 +Xa21 transgene mock
SA00027420449Taipei 309 +Xa21 transgene mock
SA00027520459Taipei 309 +Xa21 transgene mock
SA00027620444Taipei 309 +Xa21 transgene mock
SA00027720454Taipei 309 +Xa21 transgene mock
SA00024520526Taipei 309 +Xa21 transgene no treatment
SA00024620536Taipei 309 +Xa21 transgene no treatment
SA00024720551Taipei 309 +Xa21 transgene no treatment
SA00024820561Taipei 309 +Xa21 transgene no treatment
SA00024920541Taipei 309 +Xa21 transgene no treatment
SA00025020566Taipei 309 +Xa21 transgene no treatment
SA00025120531Taipei 309 +Xa21 transgene no treatment
SA00025220546Taipei 309 +Xa21 transgene no treatment
SA00025320556Taipei 309 +Xa21 transgene no treatment
SA00025420204Taipei 309 +Xa21 transgene Pxo99
SA00025520306Taipei 309 +Xa21 transgene Pxo99
SA00025620296Taipei 309 +Xa21 transgene Pxo99
SA00025720209Taipei 309 +Xa21 transgene Pxo99
SA00025820184Taipei 309 +Xa21 transgene Pxo99
SA00025920199Taipei 309 +Xa21 transgene Pxo99
SA00026020301Taipei 309 +Xa21 transgene Pxo99
SA00026120189Taipei 309 +Xa21 transgene Pxo99
SA00026220194Taipei 309 +Xa21 transgene Pxo99
SA00028720372Taipei 309 +Xa21 transgene RaxSt
SA00028820367Taipei 309 +Xa21 transgene RaxSt
SA00028920357Taipei 309 +Xa21 transgene RaxSt
SA00029020382Taipei 309 +Xa21 transgene RaxSt
SA00029120352Taipei 309 +Xa21 transgene RaxSt
SA00029220362Taipei 309 +Xa21 transgene RaxSt
SA00029320377Taipei 309 +Xa21 transgene RaxSt
SA00029420342Taipei 309 +Xa21 transgene RaxSt
SA00029520347Taipei 309 +Xa21 transgene RaxSt
SA00029620418Taipei 309 mock
SA00029720388Taipei 309 mock
SA00029820423Taipei 309 mock
SA00029920403Taipei 309 mock
SA00030020428Taipei 309 mock
SA00030120408Taipei 309 mock
SA00030220413Taipei 309 mock
SA00030320398Taipei 309 mock
SA00030420393Taipei 309 mock
SA00026320505Taipei 309 no treatment
SA00026420510Taipei 309 no treatment
SA00026520500Taipei 309 no treatment
SA00026620485Taipei 309 no treatment
SA00026720480Taipei 309 no treatment
SA00026820495Taipei 309 no treatment
SA00026920490Taipei 309 no treatment
SA00027020515Taipei 309 no treatment
SA00027120520Taipei 309 no treatment
SA00027820153Taipei 309 Pxo99
SA00027920173Taipei 309 Pxo99
SA00028020286Taipei 309 Pxo99
SA00028120281Taipei 309 Pxo99
SA00028220163Taipei 309 Pxo99
SA00028320168Taipei 309 Pxo99
SA00028420291Taipei 309 Pxo99
SA00028520178Taipei 309 Pxo99
SA00028620158Taipei 309 Pxo99
Showing results 1 to 60 of 60


Collection ID:CO000007
Collection Summary:-
Sample Type:Plant


Treatment ID:TR000012
Treatment Protocol Comments:no treatment | Pxo99 | mock | RaxSt

Sample Preparation:

Sampleprep ID:SP000017
Sampleprep Summary:-

Combined analysis:

Analysis ID AN000021
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Units peak height


Chromatography ID:CH000007
Instrument Name:Agilent 6890N
Chromatography Type:GC


MS ID:MS000021
Analysis ID:AN000021
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI