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MB Sample ID: SA096529
| Local Sample ID: | OXGF14b-4-24h-1 |
| Subject ID: | SU001405 |
| Subject Type: | Plant |
| Subject Species: | Oryza sativa Japonica Group |
| Taxonomy ID: | 39947 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001405 |
| Subject Type: | Plant |
| Subject Species: | Oryza sativa Japonica Group |
| Taxonomy ID: | 39947 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| OXGF14b-4-24h-1 | SA096529 | FL013615 | OsGF14b-overexpression line 4 | Genotype |
| OXGF14b-4-24h-1 | SA096529 | FL013615 | 24h | Treatment |
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 |
