{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001330","ANALYSIS_ID":"AN002217","VERSION":"1","CREATED_ON":"March 22, 2020, 8:59 pm"},

"PROJECT":{"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"},

"STUDY":{"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.","EMAIL":"shijuan@agrogene.ac.cn","PHONE":"+86-020-38213643"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Oryza sativa Japonica Group","TAXONOMY_ID":"39947"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-0h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-0h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-0h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-0h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-0h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-0h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-0h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-0h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-0h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-0h-5"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-0h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-0h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-0h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-0h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-0h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-0h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-0h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-0h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-0h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-0h-5"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-0h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-0h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-0h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-0h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-0h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-0h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-0h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-0h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-0h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-0h-5"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-0h-1",
"Factors":{"Genotype":"Wild-type","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-0h-1"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-0h-2",
"Factors":{"Genotype":"Wild-type","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-0h-2"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-0h-3",
"Factors":{"Genotype":"Wild-type","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-0h-3"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-0h-4",
"Factors":{"Genotype":"Wild-type","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-0h-4"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-0h-5",
"Factors":{"Genotype":"Wild-type","Treatment":"0h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-0h-5"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-24h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-24h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-24h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-24h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-24h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-24h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-24h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-24h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-2-24h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 2","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-2-24h-5"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-24h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-24h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-24h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-24h-5"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-24h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-24h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-24h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-24h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-4-24h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 4","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-4-24h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-24h-1",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-24h-1"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-24h-2",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-24h-2"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-24h-3",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-24h-3"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-24h-4",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-24h-4"}
},
{
"Subject ID":"-",
"Sample ID":"OXGF14b-6-24h-5",
"Factors":{"Genotype":"OsGF14b-overexpression line 6","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"GF14b-6-24h-5"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-24h-1",
"Factors":{"Genotype":"Wild-type","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-24h-1"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-24h-2",
"Factors":{"Genotype":"Wild-type","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-24h-2"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-24h-3",
"Factors":{"Genotype":"Wild-type","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-24h-3"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-24h-4",
"Factors":{"Genotype":"Wild-type","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-24h-4"}
},
{
"Subject ID":"-",
"Sample ID":"Nip-24h-5",
"Factors":{"Genotype":"Wild-type","Treatment":"24h"},
"Additional sample data":{"RAW_FILE_NAME":"Nip-24h-5"}
}
],
"COLLECTION":{"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_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."},

"SAMPLEPREP":{"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_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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","FLOW_RATE":"0.4 mL/min","COLUMN_TEMPERATURE":"40°C","SOLVENT_A":"Water with 0.1% formic acid","SOLVENT_B":"Acetonitrile with 0.1% formic acid"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Fusion Tribrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST001330_AN002217_Results.txt UNITS:Relative content Has m/z:Yes Has RT:Yes RT units:Minutes"}

}