Summary of Study ST001331
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST001331 |
| Study Title | Multi-omics of OsGF14b-mediated innate immunity against panicle blast in rice (part-II) |
| Study Summary | In 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 Name | Yan |
| First Name | Shijuan |
| Address | No. 20 Jinying Road, Tianhe District, Guangzhou City, Guangdong Province, 510640, China. |
| shijuan@agrogene.ac.cn | |
| Phone | +86-020-38213643 |
| Submit Date | 2020-03-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-12-31 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | SU001405 |
| Subject Type: | Plant |
| Subject Species: | Oryza sativa Japonica Group |
| Taxonomy ID: | 39947 |
Factors:
Subject type: Plant; Subject species: Oryza sativa Japonica Group (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment |
|---|---|---|---|
| SA096510 | OXGF14b-2-0h-1 | OsGF14b-overexpression line 2 | 0h |
| SA096511 | OXGF14b-2-0h-4 | OsGF14b-overexpression line 2 | 0h |
| SA096512 | OXGF14b-2-0h-5 | OsGF14b-overexpression line 2 | 0h |
| SA096513 | OXGF14b-2-0h-3 | OsGF14b-overexpression line 2 | 0h |
| SA096514 | OXGF14b-2-0h-2 | OsGF14b-overexpression line 2 | 0h |
| SA096515 | OXGF14b-2-24h-2 | OsGF14b-overexpression line 2 | 24h |
| SA096516 | OXGF14b-2-24h-3 | OsGF14b-overexpression line 2 | 24h |
| SA096517 | OXGF14b-2-24h-5 | OsGF14b-overexpression line 2 | 24h |
| SA096518 | OXGF14b-2-24h-4 | OsGF14b-overexpression line 2 | 24h |
| SA096519 | OXGF14b-2-24h-1 | OsGF14b-overexpression line 2 | 24h |
| SA096520 | OXGF14b-4-0h-5 | OsGF14b-overexpression line 4 | 0h |
| SA096521 | OXGF14b-4-0h-3 | OsGF14b-overexpression line 4 | 0h |
| SA096522 | OXGF14b-4-0h-4 | OsGF14b-overexpression line 4 | 0h |
| SA096523 | OXGF14b-4-0h-1 | OsGF14b-overexpression line 4 | 0h |
| SA096524 | OXGF14b-4-0h-2 | OsGF14b-overexpression line 4 | 0h |
| SA096525 | OXGF14b-4-24h-2 | OsGF14b-overexpression line 4 | 24h |
| SA096526 | OXGF14b-4-24h-4 | OsGF14b-overexpression line 4 | 24h |
| SA096527 | OXGF14b-4-24h-3 | OsGF14b-overexpression line 4 | 24h |
| SA096528 | OXGF14b-4-24h-5 | OsGF14b-overexpression line 4 | 24h |
| SA096529 | OXGF14b-4-24h-1 | OsGF14b-overexpression line 4 | 24h |
| SA096530 | OXGF14b-6-0h-5 | OsGF14b-overexpression line 6 | 0h |
| SA096531 | OXGF14b-6-0h-4 | OsGF14b-overexpression line 6 | 0h |
| SA096532 | OXGF14b-6-0h-1 | OsGF14b-overexpression line 6 | 0h |
| SA096533 | OXGF14b-6-0h-2 | OsGF14b-overexpression line 6 | 0h |
| SA096534 | OXGF14b-6-0h-3 | OsGF14b-overexpression line 6 | 0h |
| SA096535 | OXGF14b-6-24h-5 | OsGF14b-overexpression line 6 | 24h |
| SA096536 | OXGF14b-6-24h-2 | OsGF14b-overexpression line 6 | 24h |
| SA096537 | OXGF14b-6-24h-3 | OsGF14b-overexpression line 6 | 24h |
| SA096538 | OXGF14b-6-24h-4 | OsGF14b-overexpression line 6 | 24h |
| SA096539 | OXGF14b-6-24h-1 | OsGF14b-overexpression line 6 | 24h |
| SA096540 | Nip-0h-5 | Wild-type | 0h |
| SA096541 | Nip-0h-1 | Wild-type | 0h |
| SA096542 | Nip-0h-4 | Wild-type | 0h |
| SA096543 | Nip-0h-2 | Wild-type | 0h |
| SA096544 | Nip-0h-3 | Wild-type | 0h |
| SA096545 | Nip-24h-5 | Wild-type | 24h |
| SA096546 | Nip-24h-4 | Wild-type | 24h |
| SA096547 | Nip-24h-1 | Wild-type | 24h |
| SA096548 | Nip-24h-2 | Wild-type | 24h |
| SA096549 | Nip-24h-3 | Wild-type | 24h |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO001400 |
| 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: | TR001420 |
| 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: | SP001413 |
| 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. one fixed volume 500 μL of the unpolar phase (the upper phase) was transferred into pre-labeled 1.5 ml microcentrifuge tube. Then the samples were dried in a SpeedVac concentrator without heating. The dried 500 μL aliquot from the upper phase for lipids profiling was re-suspended in 200 μL UPLC-grade ACN: 2-propanol: dichloromethane (1:1:1, v/v/v) and analyzed using LC-MS for lipidomics study. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002219 | AN002220 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters CORTECS C18 (150 x 2.1mm,2.7um) | Waters CORTECS C18 (150 x 2.1mm,2.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Fusion Tribrid Orbitrap | Thermo Fusion Tribrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Relative content | Relative content |
Chromatography:
| Chromatography ID: | CH001628 |
| Chromatography Summary: | Five μL of each sample was eluted using a CORTECS® C18 column (150 mm × 2.1 mm, 2.7μm, Waters) with 0.4 mL/min flow rate. The mobile phase A was water: ACN (40: 60, v/v) with 0.1% formic acid and 10mM ammonium formate, and the mobile phase B was 2-propanol: ACN (90:10, v/v) with 0.1% formic acid and 10mM ammonium formate. The compounds were separated by a elution gradient: 20% B was firstly maintained for 0.2 min, then linearly decreased to 60% B from 0.2 to 2min, to 100% B from 2 to 9min, and maintained at 100% B from 9 to 10 min, then linearly increased to 20% B from 10 to 10.5 min followed by equilibration at 20% B for 3.5 min. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters CORTECS C18 (150 x 2.1mm,2.7um) |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002065 |
| Analysis ID: | AN002219 |
| Instrument Name: | Thermo Fusion Tribrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The spray voltage was set to 3500 V in the positive-ion modes, with the following ion-source properties: sheath gas, 45 Arbs; auxiliary gas, 10 Arbs; sweep gas, 0 Arbs; ion-transfer tube temperature, 320 °C; vaporizer temp, 350 °C. All FTMS data were acquired using the following conditions: detector type, orbitrap; orbitrap resolution, 120000; scan range was set to m/z 200-1200. The AGC was set at 5.0 e5 and the maximum injection time was set to 100 ms. RF lens was set to 60%, and the microscans was 1. data type, profile. All FTMS2 data were acquired using the following conditions: isolation mode, quadrupole; isolation window, 1 m/z; detector type, orbitrap; scan range, auto; AGC target, 5.0 e4; maximum injection time, 100 ms; microscans, 1; orbitrap resolution, 30000; first mass, 50 m/z; data type, profile. The HCD collision energy was set to 25% with ± HCD collision energy was set 5% in positive mode, and the HCD collision energy was set to 30% with ± HCD collision energy was set 5% in negative mode. All data was acquired by the Xcalibur 4.1 software (Thermo Fisher Scientific, USA). Thermo Scientific™ LipidSearch™ 5.0 software was used for lipidome data processing. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002066 |
| Analysis ID: | AN002220 |
| Instrument Name: | Thermo Fusion Tribrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The spray voltage was set to -3000 V in the negative-ion modes, with the following ion-source properties: sheath gas, 45 Arbs; auxiliary gas, 10 Arbs; sweep gas, 0 Arbs; ion-transfer tube temperature, 320 °C; vaporizer temp, 350 °C. All FTMS data were acquired using the following conditions: detector type, orbitrap; orbitrap resolution, 120000; scan range was set to m/z 200-1200. The AGC was set at 5.0 e5 and the maximum injection time was set to 100 ms. RF lens was set to 60%, and the microscans was 1. data type, profile. All FTMS2 data were acquired using the following conditions: isolation mode, quadrupole; isolation window, 1 m/z; detector type, orbitrap; scan range, auto; AGC target, 5.0 e4; maximum injection time, 100 ms; microscans, 1; orbitrap resolution, 30000; first mass, 50 m/z; data type, profile. The HCD collision energy was set to 25% with ± HCD collision energy was set 5% in positive mode, and the HCD collision energy was set to 30% with ± HCD collision energy was set 5% in negative mode. All data was acquired by the Xcalibur 4.1 software (Thermo Fisher Scientific, USA). Thermo Scientific™ LipidSearch™ 5.0 software was used for lipidome data processing. |
| Ion Mode: | NEGATIVE |
