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.
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 | ST001330 |
| Study Title | Multi-omics of OsGF14b-mediated innate immunity against panicle blast in rice |
| 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 | GC-MS/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: | SU001404 |
| 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 |
|---|---|---|---|
| SA096470 | OXGF14b-2-0h-1 | OsGF14b-overexpression line 2 | 0h |
| SA096471 | OXGF14b-2-0h-4 | OsGF14b-overexpression line 2 | 0h |
| SA096472 | OXGF14b-2-0h-5 | OsGF14b-overexpression line 2 | 0h |
| SA096473 | OXGF14b-2-0h-3 | OsGF14b-overexpression line 2 | 0h |
| SA096474 | OXGF14b-2-0h-2 | OsGF14b-overexpression line 2 | 0h |
| SA096475 | OXGF14b-2-24h-2 | OsGF14b-overexpression line 2 | 24h |
| SA096476 | OXGF14b-2-24h-3 | OsGF14b-overexpression line 2 | 24h |
| SA096477 | OXGF14b-2-24h-5 | OsGF14b-overexpression line 2 | 24h |
| SA096478 | OXGF14b-2-24h-4 | OsGF14b-overexpression line 2 | 24h |
| SA096479 | OXGF14b-2-24h-1 | OsGF14b-overexpression line 2 | 24h |
| SA096480 | OXGF14b-4-0h-5 | OsGF14b-overexpression line 4 | 0h |
| SA096481 | OXGF14b-4-0h-3 | OsGF14b-overexpression line 4 | 0h |
| SA096482 | OXGF14b-4-0h-4 | OsGF14b-overexpression line 4 | 0h |
| SA096483 | OXGF14b-4-0h-1 | OsGF14b-overexpression line 4 | 0h |
| SA096484 | OXGF14b-4-0h-2 | OsGF14b-overexpression line 4 | 0h |
| SA096485 | OXGF14b-4-24h-2 | OsGF14b-overexpression line 4 | 24h |
| SA096486 | OXGF14b-4-24h-4 | OsGF14b-overexpression line 4 | 24h |
| SA096487 | OXGF14b-4-24h-3 | OsGF14b-overexpression line 4 | 24h |
| SA096488 | OXGF14b-4-24h-5 | OsGF14b-overexpression line 4 | 24h |
| SA096489 | OXGF14b-4-24h-1 | OsGF14b-overexpression line 4 | 24h |
| SA096490 | OXGF14b-6-0h-5 | OsGF14b-overexpression line 6 | 0h |
| SA096491 | OXGF14b-6-0h-4 | OsGF14b-overexpression line 6 | 0h |
| SA096492 | OXGF14b-6-0h-1 | OsGF14b-overexpression line 6 | 0h |
| SA096493 | OXGF14b-6-0h-2 | OsGF14b-overexpression line 6 | 0h |
| SA096494 | OXGF14b-6-0h-3 | OsGF14b-overexpression line 6 | 0h |
| SA096495 | OXGF14b-6-24h-5 | OsGF14b-overexpression line 6 | 24h |
| SA096496 | OXGF14b-6-24h-2 | OsGF14b-overexpression line 6 | 24h |
| SA096497 | OXGF14b-6-24h-3 | OsGF14b-overexpression line 6 | 24h |
| SA096498 | OXGF14b-6-24h-4 | OsGF14b-overexpression line 6 | 24h |
| SA096499 | OXGF14b-6-24h-1 | OsGF14b-overexpression line 6 | 24h |
| SA096500 | Nip-0h-5 | Wild-type | 0h |
| SA096501 | Nip-0h-1 | Wild-type | 0h |
| SA096502 | Nip-0h-4 | Wild-type | 0h |
| SA096503 | Nip-0h-2 | Wild-type | 0h |
| SA096504 | Nip-0h-3 | Wild-type | 0h |
| SA096505 | Nip-24h-5 | Wild-type | 24h |
| SA096506 | Nip-24h-4 | Wild-type | 24h |
| SA096507 | Nip-24h-1 | Wild-type | 24h |
| SA096508 | Nip-24h-2 | Wild-type | 24h |
| SA096509 | Nip-24h-3 | Wild-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℃ |
Combined analysis:
| Analysis ID | AN002216 | AN002217 | AN002218 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | GC | Reversed phase | Reversed phase |
| Chromatography system | Agilent 7890A | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Agilent DB35-MS (30m x 0.25mm,0.25um) | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | EI | ESI | ESI |
| MS instrument type | Single quadrupole | Orbitrap | Orbitrap |
| MS instrument name | Agilent 5975 | Thermo Fusion Tribrid Orbitrap | Thermo Fusion Tribrid Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE |
| Units | Relative content | Relative content | Relative content |
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 |
MS:
| MS ID: | MS002062 |
| Analysis ID: | AN002216 |
| Instrument Name: | Agilent 5975 |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | The transfer line temperature was set to 300°C, and the ion source temperature was set to 230°C. The mass range analyzed was from m/z 85 to 700. The Agilent MassHunter Qualitative Analysis (version B06.00) software and the Agilent MassHunter Quantitative Analysis (version B.07.01) were jointly used for GC-MS data analyses. NIST library and in-house database established using authentic standards were used together for metabolite identification. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002063 |
| Analysis ID: | AN002217 |
| 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: ion source type, H-ESI; Sheath gas, 45 Arb; Aux gas, 10 Arb; sweep gas, 0 Arbs; Ion transfer tube temperature, 320 °C; Vaporizer temperature, 350 °C. Full scan data was acquired with a scan range of m/z 100-1000, which was acquired with orbitrap resolution of 120000. The automatic gain control (AGC) was set at 2E5 and the maximum injection time was set to 100 ms. RF lens was set to 60%, and the micro scans was 1. data type, profile. All FTMS2 data were acquired using the following conditions: isolation mode, quadrupole; isolation window, 1.6 m/z; detector type, Orbitrap; scan range, auto; AGC target, 5.0e4; maximum injection time, 35 ms; microscans, 1; orbitrap resolution, 15000; first mass, 100 m/z; data type, profile. Both HCD and CID were used for FTMS2 as the activation type. The HCD collision energy was set to 30%, 40%, and 50%, respectively, which ± HCD collision energy was set 10%. The CID collision energy was set to 30% and 40%, and the activation Q was set to 0.25. The Xcalibur v4.1 software (Thermo Fisher Scientific, USA) were used for HPLC-MS control. Compound Discovery (Thermo Fisher Scientific, San Jose, CA, USA) and Trace Finder 3.3 (Thermo Fisher Scientific, San Jose, CA, USA) were used for the LC-MS-based secondary metabolome data analysis, combining qualitative and quantitative analysis. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002064 |
| Analysis ID: | AN002218 |
| 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: ion source type, H-ESI; Sheath gas, 45 Arb; Aux gas, 10 Arb; sweep gas, 0 Arbs; Ion transfer tube temperature, 320 °C; Vaporizer temperature, 350 °C. Full scan data was acquired with a scan range of m/z 100-1000, which was acquired with orbitrap resolution of 120000. The automatic gain control (AGC) was set at 2E5 and the maximum injection time was set to 100 ms. RF lens was set to 60%, and the micro scans was 1. data type, profile. All FTMS2 data were acquired using the following conditions: isolation mode, quadrupole; isolation window, 1.6 m/z; detector type, Orbitrap; scan range, auto; AGC target, 5.0e4; maximum injection time, 35 ms; microscans, 1; orbitrap resolution, 15000; first mass, 100 m/z; data type, profile. Both HCD and CID were used for FTMS2 as the activation type. The HCD collision energy was set to 30%, 40%, and 50%, respectively, which ± HCD collision energy was set 10%. The CID collision energy was set to 30% and 40%, and the activation Q was set to 0.25. The Xcalibur v4.1 software (Thermo Fisher Scientific, USA) were used for HPLC-MS control. Compound Discovery (Thermo Fisher Scientific, San Jose, CA, USA) and Trace Finder 3.3 (Thermo Fisher Scientific, San Jose, CA, USA) were used for the LC-MS-based secondary metabolome data analysis, combining qualitative and quantitative analysis. |
| Ion Mode: | NEGATIVE |
