Summary of Study ST001330

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000909. The data can be accessed directly via it's Project DOI: 10.21228/M8668V This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001330
Study TitleMulti-omics of OsGF14b-mediated innate immunity against panicle blast in rice
Study SummaryIn the present study, we used a multi-omics approach to decipher the molecular mechanisms of OsGF14b in governing panicle resistance to Magnaporthe oryzae.Results revealed OsGF14b mediated panicle blast resistance was involved in the activation of auxin and JA signaling pathways, resulting in reprogramming of the phenylpropanoid and diterpenoid pathway.
Institute
Agro-biological Gene Research Center , Guangdong Academy of Agricultural Sciences
Last NameYan
First NameShijuan
AddressNo. 20 Jinying Road, Tianhe District, Guangzhou City, Guangdong Province, 510640, China.
Emailshijuan@agrogene.ac.cn
Phone+86-020-38213643
Submit Date2020-03-13
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailGC-MS/LC-MS
Release Date2020-12-31
Release Version1
Shijuan Yan Shijuan Yan
https://dx.doi.org/10.21228/M8668V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000909
Project DOI:doi: 10.21228/M8668V
Project Title:Rice panicle blast resistence
Project Summary:Metabolomics studies of OsGF14b-mediated innate immunity against panicle blast in rice
Institute:Guangdong Academy of Agricultural Sciences
Department:Agro-biological Gene Research Center
Last Name:Yan
First Name:Shijuan
Address:No. 20 Jinying Road, Tianhe District, Guangzhou City, Guangdong Province, 510640, China.
Email:shijuan@agrogene.ac.cn
Phone:+86-020-38213643

Subject:

Subject ID:SU001404
Subject Type:Plant
Subject Species:Oryza sativa Japonica Group
Taxonomy ID:39947
Species Group:Plants

Factors:

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

mb_sample_id local_sample_id Genotype Treatment
SA096470OXGF14b-2-0h-1OsGF14b-overexpression line 2 0h
SA096471OXGF14b-2-0h-4OsGF14b-overexpression line 2 0h
SA096472OXGF14b-2-0h-5OsGF14b-overexpression line 2 0h
SA096473OXGF14b-2-0h-3OsGF14b-overexpression line 2 0h
SA096474OXGF14b-2-0h-2OsGF14b-overexpression line 2 0h
SA096475OXGF14b-2-24h-2OsGF14b-overexpression line 2 24h
SA096476OXGF14b-2-24h-3OsGF14b-overexpression line 2 24h
SA096477OXGF14b-2-24h-5OsGF14b-overexpression line 2 24h
SA096478OXGF14b-2-24h-4OsGF14b-overexpression line 2 24h
SA096479OXGF14b-2-24h-1OsGF14b-overexpression line 2 24h
SA096480OXGF14b-4-0h-5OsGF14b-overexpression line 4 0h
SA096481OXGF14b-4-0h-3OsGF14b-overexpression line 4 0h
SA096482OXGF14b-4-0h-4OsGF14b-overexpression line 4 0h
SA096483OXGF14b-4-0h-1OsGF14b-overexpression line 4 0h
SA096484OXGF14b-4-0h-2OsGF14b-overexpression line 4 0h
SA096485OXGF14b-4-24h-2OsGF14b-overexpression line 4 24h
SA096486OXGF14b-4-24h-4OsGF14b-overexpression line 4 24h
SA096487OXGF14b-4-24h-3OsGF14b-overexpression line 4 24h
SA096488OXGF14b-4-24h-5OsGF14b-overexpression line 4 24h
SA096489OXGF14b-4-24h-1OsGF14b-overexpression line 4 24h
SA096490OXGF14b-6-0h-5OsGF14b-overexpression line 6 0h
SA096491OXGF14b-6-0h-4OsGF14b-overexpression line 6 0h
SA096492OXGF14b-6-0h-1OsGF14b-overexpression line 6 0h
SA096493OXGF14b-6-0h-2OsGF14b-overexpression line 6 0h
SA096494OXGF14b-6-0h-3OsGF14b-overexpression line 6 0h
SA096495OXGF14b-6-24h-5OsGF14b-overexpression line 6 24h
SA096496OXGF14b-6-24h-2OsGF14b-overexpression line 6 24h
SA096497OXGF14b-6-24h-3OsGF14b-overexpression line 6 24h
SA096498OXGF14b-6-24h-4OsGF14b-overexpression line 6 24h
SA096499OXGF14b-6-24h-1OsGF14b-overexpression line 6 24h
SA096500Nip-0h-5Wild-type 0h
SA096501Nip-0h-1Wild-type 0h
SA096502Nip-0h-4Wild-type 0h
SA096503Nip-0h-2Wild-type 0h
SA096504Nip-0h-3Wild-type 0h
SA096505Nip-24h-5Wild-type 24h
SA096506Nip-24h-4Wild-type 24h
SA096507Nip-24h-1Wild-type 24h
SA096508Nip-24h-2Wild-type 24h
SA096509Nip-24h-3Wild-type 24h
Showing results 1 to 40 of 40

Collection:

Collection ID:CO001399
Collection Summary:The panicles at the initial heading stage of the wild-type Nipponbare (Nip) and OsGF14b-overexpressing plants were harvested before (Nip-0h; OXGF14b-2-0h; OXGF14b-4-0h; OXGF14b-6-0h) and after M. oryzae 24-hour inoculation (Nip-24h; OXGF14b-2-24h; OXGF14b-4-24h; OXGF14b-6-24h) respectively. They were immediately frozen in liquid nitrogen, with each biological replicate containing panicle pooled from 10 individual plants.
Sample Type:Seeds

Treatment:

Treatment ID:TR001419
Treatment Summary:Wild-type japonica rice (Oryzae sativa cv. Nipponbare) and three OsGF14b gene overexpressing lines, including transgenic line 2 (OXGF14b-2), transgenic line 4 (OXGF14b-4), transgenic line 6 (OXGF14b-6) were used in this study. Rice seeds were surface-sterilized and transferred to 1/2 MS medium and incubated in a growth chamber for germination under light of 200 μmol/m2/s with a 12-h photoperiod at 26℃. Subsequently, rice seedlings were transplanted into soil and kept in a greenhouse. M. oryzae GD08-T13 was used for rice blast inoculation.

Sample Preparation:

Sampleprep ID:SP001412
Sampleprep Summary:The rice panicle pre-cooled in liquid nitrogen were ground using a Mixer/mill (MM400; Retsch) with steel ball for 30 seconds at 30 HZ. Fifty milligram of rice panicle powder of each sample was extracted with a fixed volume (1 ml) of pre-cooled (−20 °C) extraction solvent (methanol: chloroform: water = 5: 2: 2) was added to homogenized tissues. After adding the extraction solvent, the vials/tubes were thoroughly vortexed for 1 min and then incubated on an orbital shaker (200 rpm) for 10 min at 4 °C followed by a 15 min sonication step. For phase separation, a volume of 500 µl of solvent (methanol: water = 1: 3), was added to each vial/tube and the samples were again thoroughly vortexed for 1 min. After that, the samples are centrifuged at a speed of 14000rpm for 10 min at 4 °C. Two fixed volume of 200 μL of the polar phase (the lower phase) were transferred into pre-labeled 1.5 ml microcentrifuge tube respectively. Then the samples were dried in a SpeedVac concentrator without heating. Two dried 200 μL aliquots of the polar phase in each sample were analyzed using gas chromatography tandem mass spectrometry (GC-MS) and liquid chromatography tandem mass spectrometry (LC-MS) for metabolomics study. The dried 200 µl aliquots of the polar phase for GC-MS analysis were re-suspended in methoxyamine-hydrochloride/pyridine solution for methoxymization of carbonyl groups followed by heating at 37 °C for 2 h. The samples were further derivatized with N-methyl-N-trimethylsilyltrifloracetamide (MSTFA) for 30 min at 37 °C. then one µl of the derivatized sample mixture was injected onto the GC-column and measured. Another dried 200 µl aliquots of the polar phase were re-suspended in 150 µl UPLC-grade methanol: water (1:1, vol/vol) and subjected to LC-MS analysis.
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Chromatography:

Chromatography ID:CH001626
Chromatography Summary:One µl was taken from each sample and injected into GC-MS at 270°C in a split mode (50: 1) with helium carrier gas (> 99.999% purity) flow set to 1 ml/min, and separated by a DB-35MS UI (30 m × 0.25 mm, 0.25 µm) capillary column. The temperature was isothermal for 4 min at 90°C, followed by an 8°C per min ramp up to 205°C, then held for 2 min, and finally ramped up at a rate of 15°C per min to 310°C, held for 2 min.
Instrument Name:Agilent 7890A
Column Name:Agilent DB35-MS (30m x 0.25mm,0.25um)
Chromatography Type:GC
  
Chromatography ID:CH001627
Chromatography Summary:Firstly, 10 μL of each sample was eluted using a TSS T3 column (100 mm × 2.1 mm containing 1.8 μm diameter particles, Waters) with 0.4 mL/min flow rate. The mobile phase A was water with 0.1% formic acid, and the mobile phase B was ACN with 0.1% formic acid. The compounds were separated by a elution gradient: 1% B was initially firstly maintained for 1 min, then linearly increased to 40% B from 1 to 11 min, to 70% B from 11 to 13 min, then to 99% B from 13 to 15 min, and maintained at 99% B from 15 to 16 min, then linearly decreased to 1% B from 16 to 17 min followed by equilibration at 1% B for 3 min. and the column temperature was set at 40°C.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40°C
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN002216
Analysis Type:MS
Chromatography ID:CH001626
Num Factors:8
Has Rt:1
Rt Units:Minutes
Results File:ST001330_AN002216_Results.txt
Units:Relative content
  
Analysis ID:AN002217
Analysis Type:MS
Chromatography ID:CH001627
Num Factors:8
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST001330_AN002217_Results.txt
Units:Relative content
  
Analysis ID:AN002218
Analysis Type:MS
Chromatography ID:CH001627
Num Factors:8
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST001330_AN002218_Results.txt
Units:Relative content
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