{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001305","ANALYSIS_ID":"AN002174","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Intergrated Metabolomics and Transcriptomics Suggest Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica","PROJECT_TYPE":"Comparison","PROJECT_SUMMARY":"Bacterial extractions from WT and 2-iminobutanoate/2iminopropanoate deaminase (RidA) KO S. Enterica lines","INSTITUTE":"University of Georgia","DEPARTMENT":"CCRC","LAST_NAME":"Walejko","FIRST_NAME":"Jacquelyn","ADDRESS":"315 Riverbend Road, Rm 1045, Athens GA 30602","EMAIL":"jacquelyn.walejko@duke.edu","PHONE":"9194792304","DOI":"http://dx.doi.org/10.21228/M85D77"},

"STUDY":{"STUDY_TITLE":"Integrated Metabolomics and Transcriptomics Suggest the Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica","STUDY_SUMMARY":"NMR metabolomics of bacterial extractions from WT and 2-iminobutanoate/2iminopropanoate deaminase (RidA) KO S. Enterica lines","INSTITUTE":"University of Georgia","DEPARTMENT":"CCRC","LAST_NAME":"Edison","FIRST_NAME":"Arthur","ADDRESS":"315 Riverbend Road, Athens, GA 30602","EMAIL":"aedison@uga.edu","PHONE":"7065428156","SUBMIT_DATE":"2020-01-09"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Salmonella enterica","TAXONOMY_ID":"28901"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"RidA1",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"3"}
},
{
"Subject ID":"-",
"Sample ID":"RidA2",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"4"}
},
{
"Subject ID":"-",
"Sample ID":"RidA3",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"5"}
},
{
"Subject ID":"-",
"Sample ID":"RidA4",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"6"}
},
{
"Subject ID":"-",
"Sample ID":"RidA5",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"9"}
},
{
"Subject ID":"-",
"Sample ID":"RidA6",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"10"}
},
{
"Subject ID":"-",
"Sample ID":"RidA7",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"12"}
},
{
"Subject ID":"-",
"Sample ID":"RidA8",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"16"}
},
{
"Subject ID":"-",
"Sample ID":"RidA9",
"Factors":{"Strain":"RidA KO"},
"Additional sample data":{"RAW_FILE_NAME":"17"}
},
{
"Subject ID":"-",
"Sample ID":"WT1",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"1"}
},
{
"Subject ID":"-",
"Sample ID":"WT2",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"2"}
},
{
"Subject ID":"-",
"Sample ID":"WT3",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"7"}
},
{
"Subject ID":"-",
"Sample ID":"WT4",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"8"}
},
{
"Subject ID":"-",
"Sample ID":"WT5",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"11"}
},
{
"Subject ID":"-",
"Sample ID":"WT6",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"13"}
},
{
"Subject ID":"-",
"Sample ID":"WT7",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"14"}
},
{
"Subject ID":"-",
"Sample ID":"WT8",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"15"}
},
{
"Subject ID":"-",
"Sample ID":"WT9",
"Factors":{"Strain":"WT"},
"Additional sample data":{"RAW_FILE_NAME":"18"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Ten biologically independent cultures each of wild-type (DM9404) and ridA mutant (DM3480) strains were grown overnight in NB medium at 37 °C and used to inoculate (1% inoculum) 250 mL minimal glucose medium in 500 mL non-baffled flasks. Flasks were randomly arranged in an Innova®44 incubator and cultures were allowed to grow 16 h shaking at 180 RPM and 37 °C. Cultures were cooled on ice 5 min and then harvested by centrifugation at 7,000 x G for 10 min at 4 °C. The supernatant was decanted, pellets were resuspended in 10 mL ddH2O and transferred to sterile 15 mL conical tubes in which they were pelleted at 7,000 x G 10 min at 4 °C. Final supernatant was decanted and pellets were frozen in liquid nitrogen and stored at -80 °C prior to cell extractions.","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"These samples did not undergo addition treatment."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Each frozen bacterial pellet (~1 g) was thawed on ice and homogenized 3 times. For homogenization, 2.6 g of 0.1 mm zirconium beads and 6 mL 4 C MeOH/H2O (80/20) solvent was added and samples were agitated 7 times (210 s total) at 1600 rpm in a FastPrep 96 (MPBIO). Samples were then centrifuged at 416 g and 4 C for 16 min and supernatant was transferred to a new 15 mL conical tube. Homogenization was carried out a second and third time using 4 mL MeOH/H2O with 4 homogenization cycles (150 s) and 2 mL MeOH/H2O with 3 homogenization cycles (150 s), respectively. Pooled supernatants from each sample were concentrated to dryness using a CentriVap Benchtop Vacuum Concentrator (Labconco). The extracts were reconstituted in 600 L of deuterated 100 mM sodium phosphate buer (pH 7.4) containing 1 mM of the internal standard DSS (d6 4,4-dimethyl-4-silapentane-1-sulfonic acid) and vortex mixed 2 min. Each sample was transferred into 5 mm SampleJet NMR tubes for NMR analysis."},

"CHROMATOGRAPHY":[],

"ANALYSIS":{"LABORATORY_NAME":"Complex Carbohydrate Research Center NMR Facility","ANALYSIS_TYPE":"NMR","OPERATOR_NAME":"Adrien Le Guennec"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance III HD","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"800 MHz"},

"NMR_METABOLITE_DATA":{
"Units":"Area under curve",

"Data":[{"Metabolite":"2-Aminobutyric acid","RidA1":"1.0584","RidA2":"1.1712","RidA3":"1.1595","RidA4":"1.0960","RidA5":"0.9905","RidA6":"1.3299","RidA7":"1.1182","RidA8":"1.1430","RidA9":"1.1786","WT1":"1.7456","WT2":"0.7645","WT3":"0.8580","WT4":"1.7344","WT5":"1.8076","WT6":"0.9397","WT7":"0.8712","WT8":"0.8914","WT9":"0.9132"},{"Metabolite":"2-isopropylmalic acid","RidA1":"0.7678","RidA2":"1.4187","RidA3":"1.5349","RidA4":"0.5799","RidA5":"1.5595","RidA6":"1.5746","RidA7":"1.6952","RidA8":"1.7450","RidA9":"0.8039","WT1":"0.3563","WT2":"0.2590","WT3":"0.2694","WT4":"0.3355","WT5":"0.4028","WT6":"0.3165","WT7":"0.3387","WT8":"0.3208","WT9":"0.3017"},{"Metabolite":"2-oxoglutaric acid","RidA1":"0.0179","RidA2":"0.0195","RidA3":"0.0176","RidA4":"0.0205","RidA5":"0.1232","RidA6":"0.0380","RidA7":"0.5135","RidA8":"0.0223","RidA9":"0.0195","WT1":"0.0647","WT2":"0.0223","WT3":"0.4088","WT4":"0.0193","WT5":"0.0646","WT6":"0.0904","WT7":"0.0240","WT8":"0.0270","WT9":"0.0327"},{"Metabolite":"Acetate","RidA1":"1.8481","RidA2":"2.0381","RidA3":"1.9932","RidA4":"1.9802","RidA5":"2.1387","RidA6":"2.2753","RidA7":"2.2566","RidA8":"2.4532","RidA9":"2.0882","WT1":"2.2417","WT2":"2.5891","WT3":"2.2490","WT4":"2.2684","WT5":"2.2375","WT6":"2.6679","WT7":"2.8998","WT8":"2.6049","WT9":"2.7555"},{"Metabolite":"Adenosine monophosphate (AMP)","RidA1":"0.4319","RidA2":"0.3632","RidA3":"0.3641","RidA4":"0.3939","RidA5":"0.4854","RidA6":"0.4068","RidA7":"0.4292","RidA8":"0.4181","RidA9":"0.4915","WT1":"0.7440","WT2":"0.8031","WT3":"0.4742","WT4":"0.8133","WT5":"0.6335","WT6":"0.9117","WT7":"0.6717","WT8":"0.7351","WT9":"0.5333"},{"Metabolite":"Alanine","RidA1":"0.5503","RidA2":"0.6062","RidA3":"0.5957","RidA4":"0.7053","RidA5":"0.8121","RidA6":"0.5828","RidA7":"0.7299","RidA8":"0.8767","RidA9":"0.6696","WT1":"0.6371","WT2":"0.3598","WT3":"0.6637","WT4":"0.7472","WT5":"0.6537","WT6":"0.6007","WT7":"0.4255","WT8":"0.5537","WT9":"0.5934"},{"Metabolite":"CMP","RidA1":"0.1456","RidA2":"0.1382","RidA3":"0.1458","RidA4":"0.1228","RidA5":"0.1166","RidA6":"0.1579","RidA7":"0.1387","RidA8":"0.1092","RidA9":"0.1341","WT1":"0.0160","WT2":"0.0590","WT3":"0.0482","WT4":"0.0221","WT5":"0.0253","WT6":"0.0689","WT7":"0.0592","WT8":"0.0668","WT9":"0.0455"},{"Metabolite":"CTP","RidA1":"0.2097","RidA2":"0.2171","RidA3":"0.1859","RidA4":"0.1562","RidA5":"0.1954","RidA6":"0.2477","RidA7":"0.2412","RidA8":"0.1602","RidA9":"0.1576","WT1":"0.2286","WT2":"0.2312","WT3":"0.1879","WT4":"0.1650","WT5":"0.2552","WT6":"0.2287","WT7":"0.2001","WT8":"0.2221","WT9":"0.1401"},{"Metabolite":"Cytidine diphosphate (CDP)","RidA1":"0.0221","RidA2":"0.0221","RidA3":"0.0196","RidA4":"0.0151","RidA5":"0.0099","RidA6":"0.0265","RidA7":"0.0225","RidA8":"0.0101","RidA9":"0.0076","WT1":"0.0146","WT2":"0.0113","WT3":"0.0108","WT4":"0.0055","WT5":"0.0163","WT6":"0.0183","WT7":"0.0148","WT8":"0.0170","WT9":"0.0062"},{"Metabolite":"dCMP","RidA1":"0.5212","RidA2":"0.4366","RidA3":"0.4400","RidA4":"0.4295","RidA5":"0.4383","RidA6":"0.4502","RidA7":"0.4336","RidA8":"0.3937","RidA9":"0.4513","WT1":"0.7172","WT2":"0.7915","WT3":"0.6448","WT4":"0.7114","WT5":"0.6160","WT6":"0.7455","WT7":"0.6756","WT8":"0.6992","WT9":"0.5144"},{"Metabolite":"Ethanolamine","RidA1":"0.0286","RidA2":"0.0315","RidA3":"0.0381","RidA4":"0.0426","RidA5":"0.0472","RidA6":"0.0370","RidA7":"0.0333","RidA8":"0.0815","RidA9":"0.0401","WT1":"0.0259","WT2":"0.0553","WT3":"0.0352","WT4":"0.0632","WT5":"0.0325","WT6":"0.0149","WT7":"0.0344","WT8":"0.0320","WT9":"0.0368"},{"Metabolite":"Formate","RidA1":"0.1223","RidA2":"0.0983","RidA3":"0.1143","RidA4":"0.1165","RidA5":"0.1002","RidA6":"0.1378","RidA7":"0.1189","RidA8":"0.1352","RidA9":"0.1640","WT1":"0.1664","WT2":"0.1759","WT3":"0.1497","WT4":"0.1676","WT5":"0.1712","WT6":"0.1356","WT7":"0.1856","WT8":"0.1598","WT9":"0.1497"},{"Metabolite":"Glucose","RidA1":"0.0533","RidA2":"0.0638","RidA3":"0.0640","RidA4":"0.0604","RidA5":"0.0584","RidA6":"0.0630","RidA7":"0.0580","RidA8":"0.0491","RidA9":"0.0571","WT1":"0.0460","WT2":"0.0486","WT3":"0.0437","WT4":"0.0464","WT5":"0.0497","WT6":"0.0325","WT7":"0.0380","WT8":"0.0339","WT9":"0.0369"},{"Metabolite":"Glutamate","RidA1":"0.2275","RidA2":"0.3026","RidA3":"0.2800","RidA4":"0.2176","RidA5":"0.2214","RidA6":"0.2853","RidA7":"0.1233","RidA8":"0.3434","RidA9":"0.2523","WT1":"0.2080","WT2":"0.1511","WT3":"0.1117","WT4":"0.2092","WT5":"0.2175","WT6":"0.2131","WT7":"0.1588","WT8":"0.1932","WT9":"0.1401"},{"Metabolite":"GSSG","RidA1":"2.0290","RidA2":"2.1001","RidA3":"2.0994","RidA4":"1.7015","RidA5":"1.7569","RidA6":"2.2205","RidA7":"2.2245","RidA8":"2.0262","RidA9":"1.9906","WT1":"0.7047","WT2":"0.2959","WT3":"0.2944","WT4":"0.6457","WT5":"0.9278","WT6":"0.5267","WT7":"0.5120","WT8":"0.5076","WT9":"0.4752"},{"Metabolite":"Isoleucine","RidA1":"0.2421","RidA2":"0.2201","RidA3":"0.2169","RidA4":"0.2532","RidA5":"0.2183","RidA6":"0.2035","RidA7":"0.2265","RidA8":"0.2207","RidA9":"0.2125","WT1":"0.2525","WT2":"0.3953","WT3":"0.5277","WT4":"0.2446","WT5":"0.2316","WT6":"0.5031","WT7":"0.3541","WT8":"0.4963","WT9":"0.3261"},{"Metabolite":"Leucine","RidA1":"0.8115","RidA2":"0.8509","RidA3":"0.8682","RidA4":"0.8873","RidA5":"0.7454","RidA6":"0.8407","RidA7":"0.7513","RidA8":"0.7440","RidA9":"0.7443","WT1":"1.9082","WT2":"1.8209","WT3":"2.3367","WT4":"1.7510","WT5":"1.8290","WT6":"2.1424","WT7":"1.6953","WT8":"2.1054","WT9":"1.5501"},{"Metabolite":"Lysine","RidA1":"0.0760","RidA2":"0.0860","RidA3":"0.0869","RidA4":"0.0784","RidA5":"0.0776","RidA6":"0.0445","RidA7":"0.0436","RidA8":"0.0661","RidA9":"0.0524","WT1":"0.5182","WT2":"0.7595","WT3":"0.4593","WT4":"0.5702","WT5":"0.4370","WT6":"0.7738","WT7":"0.6007","WT8":"0.6878","WT9":"0.4919"},{"Metabolite":"Malic acid","RidA1":"0.0287","RidA2":"0.0283","RidA3":"0.0279","RidA4":"0.0354","RidA5":"0.0370","RidA6":"0.0324","RidA7":"0.0359","RidA8":"0.0309","RidA9":"0.0299","WT1":"0.0315","WT2":"0.0404","WT3":"0.0432","WT4":"0.0347","WT5":"0.0339","WT6":"0.0278","WT7":"0.0397","WT8":"0.0331","WT9":"0.0424"},{"Metabolite":"Maltose","RidA1":"1.4993","RidA2":"1.5102","RidA3":"1.5347","RidA4":"1.6495","RidA5":"1.6806","RidA6":"1.5195","RidA7":"1.7021","RidA8":"1.7472","RidA9":"1.5210","WT1":"1.3653","WT2":"1.4268","WT3":"1.4939","WT4":"1.2983","WT5":"1.3343","WT6":"1.6250","WT7":"1.4356","WT8":"1.4861","WT9":"1.2618"},{"Metabolite":"Methionine","RidA1":"0.1694","RidA2":"0.1544","RidA3":"0.1693","RidA4":"0.1620","RidA5":"0.1510","RidA6":"0.1670","RidA7":"0.1558","RidA8":"0.1855","RidA9":"0.1831","WT1":"0.0767","WT2":"0.0673","WT3":"0.0596","WT4":"0.0808","WT5":"0.0923","WT6":"0.0754","WT7":"0.0779","WT8":"0.0750","WT9":"0.0752"},{"Metabolite":"N-acetyl alanine","RidA1":"0.0254","RidA2":"0.0202","RidA3":"0.0190","RidA4":"0.0261","RidA5":"0.0210","RidA6":"0.0216","RidA7":"0.0261","RidA8":"0.0181","RidA9":"0.0163","WT1":"0.0103","WT2":"0.0176","WT3":"0.0261","WT4":"0.0112","WT5":"0.0146","WT6":"0.0217","WT7":"0.0192","WT8":"0.0217","WT9":"0.0143"},{"Metabolite":"N-Acetylputrescine","RidA1":"0.1241","RidA2":"0.1313","RidA3":"0.1258","RidA4":"0.1209","RidA5":"0.1026","RidA6":"0.1281","RidA7":"0.0978","RidA8":"0.1182","RidA9":"0.1546","WT1":"0.1645","WT2":"0.1854","WT3":"0.1067","WT4":"0.1726","WT5":"0.1565","WT6":"0.1562","WT7":"0.1765","WT8":"0.1521","WT9":"0.1650"},{"Metabolite":"Nicotinamide Adenine Dinucleotide (NAD)","RidA1":"0.0807","RidA2":"0.0867","RidA3":"0.0846","RidA4":"0.0560","RidA5":"0.0541","RidA6":"0.1362","RidA7":"0.1047","RidA8":"0.0544","RidA9":"0.0642","WT1":"0.1171","WT2":"0.0941","WT3":"0.0436","WT4":"0.0486","WT5":"0.1208","WT6":"0.1201","WT7":"0.0881","WT8":"0.1171","WT9":"0.0358"},{"Metabolite":"Nicotinamide Adenine Dinucleotide Phosphate (NADP)","RidA1":"0.0430","RidA2":"0.0354","RidA3":"0.0381","RidA4":"0.0494","RidA5":"0.0383","RidA6":"0.0392","RidA7":"0.0392","RidA8":"0.0339","RidA9":"0.0363","WT1":"0.0595","WT2":"0.0541","WT3":"0.0611","WT4":"0.0533","WT5":"0.0563","WT6":"0.0431","WT7":"0.0534","WT8":"0.0503","WT9":"0.0431"},{"Metabolite":"Nicotinate Mononucleotide","RidA1":"0.3938","RidA2":"0.3597","RidA3":"0.3709","RidA4":"0.4705","RidA5":"0.4138","RidA6":"0.3277","RidA7":"0.3934","RidA8":"0.2712","RidA9":"0.2546","WT1":"0.3729","WT2":"0.2068","WT3":"0.4592","WT4":"0.3230","WT5":"0.3743","WT6":"0.2796","WT7":"0.3419","WT8":"0.2931","WT9":"0.4423"},{"Metabolite":"Pantothenic 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