{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000591","ANALYSIS_ID":"AN000906","VERSION":"1","CREATED_ON":"April 16, 2017, 6:00 pm"},

"PROJECT":{"PROJECT_TITLE":"Understanding the effects of acetyl-CoA carboxylase (ACC1) upon the metabolite profiles of Arabidopsis","PROJECT_TYPE":"Single gene knockout impact on Arabidopsis metabolites","PROJECT_SUMMARY":"The arabidopsis gene, acetyl-CoA carboxylase1 (ACC1) catalyzes the carboxylation of acetyl-CoA to malonyl-CoA. When this gene malfunctions, there are elevated levels of acetyl-CoA which have been shown to increase levels of histone acetylation. This project aims to understand how a malfunctioning ACC1 effects the levels of primary metabolites by comparing to metabolite profiles of wild type Arabidopsis grown under identical conditions.","INSTITUTE":"Agriculture and Agri-Food Canada","DEPARTMENT":"Chemistry","LABORATORY":"Renaud","LAST_NAME":"Renaud","FIRST_NAME":"Justin","ADDRESS":"1391 Sandford Street","EMAIL":"justin.renaud@agr.gc.ca","PHONE":"519-953-6698","FUNDING_SOURCE":"Natural Science and Engineering Research Council of Canada (R4019A01) and Agriculture and Agri-Food Canada A-base"},

"STUDY":{"STUDY_TITLE":"Metablomic profiling in acc1-5 mutant and wild type arabidiopsis","STUDY_SUMMARY":"This experiment tests the metabolic consequence of a mutation at the ACC1 gene (At1g36160). The allele of acc1-5 bearing an EMS mutation, which cause a single amino acid substitution from aspartic acid to asparagine. Seedlings from both the acc1-5 mutant and the wild type were harvested and analyzed via HILIC LC-MS. Of particular interest are metabolites which would be affected by depletion of malonyl-CoA pools (flavenoids) and primary metabolites.","INSTITUTE":"Agriculture and Agri-Food Canada","DEPARTMENT":"London Research and Developmental Centre","LABORATORY":"Renaud","LAST_NAME":"Renaud","FIRST_NAME":"Justin","ADDRESS":"1391 Sandford street, London, Ontario, Canada","EMAIL":"justin.renaud@agr.gc.ca","PHONE":"519-953-6698"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Arabidopsis thaliana","TAXONOMY_ID":"3702","GENOTYPE_STRAIN":"Col-0","AGE_OR_AGE_RANGE":"12 Days after germination","WEIGHT_OR_WEIGHT_RANGE":"50 mg"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WT-1",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-2",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-3",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-4",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-5",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-6",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"WT-7",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-1",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-2",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-3",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-4",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-5",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-6",
"Factors":{"Genotype":"acc1-knockout mutant"}
},
{
"Subject ID":"-",
"Sample ID":"ACC1-7",
"Factors":{"Genotype":"acc1-knockout mutant"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Arabidopsis seeds obtained from the Arabidopsis Biological Resource Center (ABRC) at the Ohio State University were grown in half strength of Murashige and Skoog (½ MS) medium (0.5XMS salts, 1.5% [w/v] sucrose, and 0.8% agar [pH 5.8]) or soil under 16h/8h light/dark cycle at 23°C. Plants were harvested 12 days after germination. 50 mg of each plant (7 mutants, 7 wild type) were ground in liquid N2 using ball mill and immediately extracted following collection protocol.","COLLECTION_PROTOCOL_FILENAME":"collection_protocol.pdf","SAMPLE_TYPE":"Seedlings","COLLECTION_LOCATION":"London, Ontario","COLLECTION_FREQUENCY":"Single"},

"TREATMENT":{"TREATMENT_SUMMARY":"Effects of single gene knockout on arabidopsis metabolites compared to wild-type control. 7 replicates of wild-type, 7-replicates of acc1-5 knockout."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"50 mg of 12 DAG WT and acc1-5 seedlings were collected and grinded in liquid N2 using a ball-mill. The fine powders were suspended in 1 mL ice cooled methanol: water (4:1) by vortex. The mixtures were sonicated in water bath sonicator for 15 mins and followed by centrifugation at 11,000g for 10 mins at 4 °C. 700 µL of the supernatant was transferred into fresh tubes and evaporated to dryness using a vacufuge at ambient temperature. The residue was re-dissolved in 1:1 mixture of methanol: water and vortexed vigorously. All samples were filtered using 0.2 μm PTFE syringe filter (Whatman) and 5 µL of 1 µg/mL 13C6 phenylalanine internal standard (Cambridge Isotopes, Tewksbury, USA) were added to all samples"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples were resolved using HILIC column","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"SeQuant ZIC- pHILIC (100 x 2.1mm, 3.5um)","FLOW_GRADIENT":"87% B for 5 minutes, decreased to 55% over 8 minutes and held for 4 minutes before returning to 87% over 3 minute","FLOW_RATE":"0.3 ml min-1","COLUMN_TEMPERATURE":"30C","SOLVENT_A":"5 mM ammonium acetate, pH = 4.00","SOLVENT_B":"B = 90% acetonitrile, 0.1% formic acid","INTERNAL_STANDARD":"13C6 phenylalanine internal standard"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Renaud","OPERATOR_NAME":"Justin Renaud","DETECTOR_TYPE":"Orbitrap"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"High resolution 140k for sample comparison. The automatic gain control (AGC) and maximum injection time (IT) were 3×106 and 524 ms respectively.","CAPILLARY_TEMPERATURE":"250°C","COLLISION_ENERGY":"-","DRY_GAS_FLOW":"30 units","FRAGMENTATION_METHOD":"HCD","ION_SOURCE_TEMPERATURE":"450","ION_SPRAY_VOLTAGE":"3.9 kV","IONIZATION":"ESI","MASS_ACCURACY":"<5 ppm","DATAFORMAT":".raw","SCANNING_RANGE":"93-1400"},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[{"Metabolite":"Valine","ACC1-1":"1251191058","ACC1-2":"1397100604","ACC1-3":"1627876569","ACC1-4":"1292553008","ACC1-5":"1209247387","ACC1-6":"1336199370","ACC1-7":"1181425154","WT-1":"431696029.5","WT-2":"445446298.7","WT-3":"455151809.2","WT-4":"350724867.5","WT-5":"378317578.8","WT-6":"540314322.1","WT-7":"576476445.7"},{"Metabolite":"Tyrosine","ACC1-1":"134351962.8","ACC1-2":"218512163.4","ACC1-3":"180005380.5","ACC1-4":"170607922.5","ACC1-5":"155543060.2","ACC1-6":"163580810.1","ACC1-7":"109258358.3","WT-1":"82419015.71","WT-2":"44701117.82","WT-3":"29766634.96","WT-4":"30866655","WT-5":"42713359.05","WT-6":"73947924.8","WT-7":"69135186.08"},{"Metabolite":"Tyramine","ACC1-1":"1197147162","ACC1-2":"820881927.8","ACC1-3":"1132435811","ACC1-4":"546423814.7","ACC1-5":"1101351042","ACC1-6":"664667667.6","ACC1-7":"598729316.1","WT-1":"432254230.9","WT-2":"329140848.2","WT-3":"425298143.8","WT-4":"187062583.6","WT-5":"245259482","WT-6":"248820956.5","WT-7":"277676472.7"},{"Metabolite":"Tryptophan","ACC1-1":"297827077.5","ACC1-2":"398002279.2","ACC1-3":"324418392.9","ACC1-4":"465241534.6","ACC1-5":"306797712.9","ACC1-6":"348849194.4","ACC1-7":"257717839.4","WT-1":"195232564.3","WT-2":"77908080.77","WT-3":"46933311.92","WT-4":"44179071.86","WT-5":"53279175.44","WT-6":"94939950.26","WT-7":"73772610.92"},{"Metabolite":"S-methylmethionine","ACC1-1":"1610436246","ACC1-2":"2067102275","ACC1-3":"1818734739","ACC1-4":"1450192851","ACC1-5":"1339751139","ACC1-6":"1205509466","ACC1-7":"1442429654","WT-1":"519343923.8","WT-2":"505639700.3","WT-3":"267291033.5","WT-4":"236062521.7","WT-5":"271195444.7","WT-6":"309762367.1","WT-7":"416003224.5"},{"Metabolite":"Serine","ACC1-1":"1096946003","ACC1-2":"1229927517","ACC1-3":"1381168529","ACC1-4":"779247104.6","ACC1-5":"835979301.1","ACC1-6":"797366995.4","ACC1-7":"814862903.4","WT-1":"434161917.4","WT-2":"332087287.4","WT-3":"399884684","WT-4":"286645734.1","WT-5":"368907664.2","WT-6":"396138912.4","WT-7":"435450279.7"},{"Metabolite":"Quercitin-glucose-rhamnoside","ACC1-1":"10802071.77","ACC1-2":"4013830.27","ACC1-3":"3882156.498","ACC1-4":"5486708.253","ACC1-5":"5648782.039","ACC1-6":"3801972.256","ACC1-7":"8703673.34","WT-1":"1860727422","WT-2":"1529994494","WT-3":"1613345784","WT-4":"852178811.6","WT-5":"1472744410","WT-6":"1276993427","WT-7":"1619422120"},{"Metabolite":"Quercitin","ACC1-1":"28614059.97","ACC1-2":"20088148.12","ACC1-3":"16921937.35","ACC1-4":"19165332.01","ACC1-5":"17921507.98","ACC1-6":"16109488.14","ACC1-7":"15745403.93","WT-1":"77549440.71","WT-2":"72362244.03","WT-3":"66696488.21","WT-4":"57739736.48","WT-5":"75561247.03","WT-6":"54054468.23","WT-7":"62542075.97"},{"Metabolite":"Proline","ACC1-1":"15089604960","ACC1-2":"4018071618","ACC1-3":"6834287705","ACC1-4":"2567818491","ACC1-5":"4332857070","ACC1-6":"5301066662","ACC1-7":"3476091855","WT-1":"2684104776","WT-2":"5335666856","WT-3":"1945452806","WT-4":"1391219217","WT-5":"1656055130","WT-6":"1836712047","WT-7":"2350402315"},{"Metabolite":"Phenylalanine","ACC1-1":"254471276.1","ACC1-2":"273747351.6","ACC1-3":"117108044.7","ACC1-4":"264243279.1","ACC1-5":"262105028.2","ACC1-6":"273809296.1","ACC1-7":"232247246","WT-1":"136098451.3","WT-2":"105722830.9","WT-3":"95394843.48","WT-4":"64047041.6","WT-5":"92659958.89","WT-6":"99829802.56","WT-7":"111425287.4"},{"Metabolite":"p-Coumaroylagmatine","ACC1-1":"23149342121","ACC1-2":"11678055396","ACC1-3":"28323122651","ACC1-4":"10577177746","ACC1-5":"9448940671","ACC1-6":"22673019232","ACC1-7":"8122146910","WT-1":"1258566850","WT-2":"1074066267","WT-3":"586149512.6","WT-4":"338572168.6","WT-5":"749630095.6","WT-6":"755026327.4","WT-7":"837450828.8"},{"Metabolite":"Ornithine","ACC1-1":"537774112.5","ACC1-2":"445965812.3","ACC1-3":"366084514.7","ACC1-4":"556246229.2","ACC1-5":"362628943.7","ACC1-6":"306122648.7","ACC1-7":"361175010.4","WT-1":"321155655.8","WT-2":"383238476.9","WT-3":"208091710.3","WT-4":"139339900.6","WT-5":"183843038.5","WT-6":"185114633.6","WT-7":"243156412.1"},{"Metabolite":"N-Acetylornithine","ACC1-1":"66257214.61","ACC1-2":"98430645.78","ACC1-3":"122088307.6","ACC1-4":"117050852.9","ACC1-5":"103481874.1","ACC1-6":"115890307.7","ACC1-7":"140310124.2","WT-1":"15688635.2","WT-2":"15507421.12","WT-3":"6859281.175","WT-4":"8009688.345","WT-5":"8973527.293","WT-6":"11182614.69","WT-7":"15746942.64"},{"Metabolite":"Methionine","ACC1-1":"172151118.1","ACC1-2":"186495690.1","ACC1-3":"203239309.1","ACC1-4":"82212787.18","ACC1-5":"80170170.27","ACC1-6":"96676437.67","ACC1-7":"93670375.05","WT-1":"133180622.1","WT-2":"74604980.36","WT-3":"64103369.8","WT-4":"48748502.38","WT-5":"68102468.82","WT-6":"53491210.41","WT-7":"51509940.33"},{"Metabolite":"Lysine","ACC1-1":"295384528.8","ACC1-2":"427963414","ACC1-3":"293660049.5","ACC1-4":"360938649.9","ACC1-5":"305351427.7","ACC1-6":"273762520","ACC1-7":"252873719.8","WT-1":"158450556.5","WT-2":"119904093.6","WT-3":"120092823.9","WT-4":"85002776.84","WT-5":"119374639.9","WT-6":"132728161.3","WT-7":"1586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-glucose-rhamnose-rhamnoside","ACC1-1":"69813227.44","ACC1-2":"37036073.64","ACC1-3":"41653211.04","ACC1-4":"43557682.26","ACC1-5":"37128435.45","ACC1-6":"39495531","ACC1-7":"30352422.18","WT-1":"696930637.5","WT-2":"639442129.2","WT-3":"508973139.9","WT-4":"281388601.7","WT-5":"451760880.1","WT-6":"506395939.9","WT-7":"512797795.2"},{"Metabolite":"Kaempferol- rhamnose- 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}

}