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"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002092","ANALYSIS_ID":"AN003417","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis","PROJECT_SUMMARY":"Untargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis.","INSTITUTE":"University of Georgia - Complex Carbohydrate Research Center","LABORATORY":"Edison Lab","LAST_NAME":"Garcia","FIRST_NAME":"Brianna","ADDRESS":"315 Riverbend Road, Athens, GA 30602","EMAIL":"brianna.garcia@uga.edu","PHONE":"7065424401","FUNDING_SOURCE":"U2CES030167","DOI":"http://dx.doi.org/10.21228/M82978","CONTRIBUTORS":"Amanda O. Shaver, Goncalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. Asef, Ricardo M. Borges, Franklin E. Leach III, Erik C. Andersen, I. Jonathan Amster, Facundo M. Fernández, Arthur S. Edison, and Lauren M. McIntyre"},

"STUDY":{"STUDY_TITLE":"Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis","STUDY_SUMMARY":"Untargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis.","INSTITUTE":"University of Georgia - Complex Carbohydrate Research Center","LABORATORY":"Edison Lab","LAST_NAME":"Garcia","FIRST_NAME":"Brianna","ADDRESS":"315 Riverbend Road","EMAIL":"brianna.garcia@uga.edu","PHONE":"7065424401","SUBMIT_DATE":"2022-02-14"},

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{
"Subject ID":"-",
"Sample ID":"b4_aos_96",
"Factors":{"Strain":"RB2550","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b4_aos_96.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_39",
"Factors":{"Strain":"RB2607","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_39.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_101",
"Factors":{"Strain":"RB2607","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_101.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_133",
"Factors":{"Strain":"RB2607","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_133.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_166",
"Factors":{"Strain":"RB2607","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_166.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_88",
"Factors":{"Strain":"RB2607","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_88.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_mutant_b1_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_mutant_b1_01.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_mutant_b1_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_mutant_b1_02.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_mutant_b2_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_mutant_b2_01.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_mutant_b2_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_mutant_b2_02.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b3_pool_mutant_b3_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b3_pool_mutant_b3_01.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b3_pool_mutant_b3_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b3_pool_mutant_b3_02.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_pool_mutant_b4_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b4_pool_mutant_b4_01.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_pool_mutant_b4_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b4_pool_mutant_b4_02.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b5_pool_mutant_b5_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b5_pool_mutant_b5_01.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_pool_mutant_b5_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b5_pool_mutant_b5_02.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_pool_mutant_b6_01",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b6_pool_mutant_b6_01.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_pool_mutant_b6_02",
"Factors":{"Strain":"-","Sample type":"pool_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"b6_pool_mutant_b6_02.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_natural_b1_01",
"Factors":{"Strain":"-","Sample type":"pool_natural"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_natural_b1_01.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_natural_b1_02",
"Factors":{"Strain":"-","Sample type":"pool_natural"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_natural_b1_02.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_natural_b2_01",
"Factors":{"Strain":"-","Sample type":"pool_natural"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_natural_b2_01.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_natural_b2_02",
"Factors":{"Strain":"-","Sample type":"pool_natural"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_natural_b2_02.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_pd1074_b1_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_pd1074_b1_01.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b1_pool_pd1074_b1_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b1_pool_pd1074_b1_02.mzML","Batch":"1","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_pd1074_b2_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_pd1074_b2_01.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b2_pool_pd1074_b2_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b2_pool_pd1074_b2_02.mzML","Batch":"2","Set":"1"}
},
{
"Subject ID":"-",
"Sample ID":"b3_pool_pd1074_b3_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b3_pool_pd1074_b3_01.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b3_pool_pd1074_b3_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b3_pool_pd1074_b3_02.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_pool_pd1074_b4_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b4_pool_pd1074_b4_01.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_pool_pd1074_b4_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b4_pool_pd1074_b4_02.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b5_pool_pd1074_b5_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b5_pool_pd1074_b5_01.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_pool_pd1074_b5_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b5_pool_pd1074_b5_02.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_pool_pd1074_b6_01",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b6_pool_pd1074_b6_01.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_pool_pd1074_b6_02",
"Factors":{"Strain":"-","Sample type":"pool_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"b6_pool_pd1074_b6_02.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b3_aos_184",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b3_aos_184.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b3_aos_42",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b3_aos_42.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b3_aos_98",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b3_aos_98.mzML","Batch":"3","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_aos_125",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b4_aos_125.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_aos_73",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b4_aos_73.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_aos_84",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b4_aos_84.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b4_aos_93",
"Factors":{"Strain":"VC1265","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b4_aos_93.mzML","Batch":"4","Set":"2"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_187",
"Factors":{"Strain":"VC2512","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_187.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_33",
"Factors":{"Strain":"VC2512","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_33.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_66",
"Factors":{"Strain":"VC2512","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_66.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_193",
"Factors":{"Strain":"VC2512","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_193.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_179",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_179.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_47",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_47.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b5_aos_70",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b5_aos_70.mzML","Batch":"5","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_105",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_105.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_85",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_85.mzML","Batch":"6","Set":"3"}
},
{
"Subject ID":"-",
"Sample ID":"b6_aos_94",
"Factors":{"Strain":"VC2524","Sample type":"sample"},
"Additional sample data":{"RAW_FILE_NAME":"b6_aos_94.mzML","Batch":"6","Set":"3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Escherichia coli (E. coli) IBAT (iterative batch average method) reference material and food source used throughout this experiment. Briefly, for each biological sample, a large-scale culture plate (LSCP) was used to generate a large mixed-stage population of worms (four to seven LSCP replicates per test strain). For each LSCP, worms were collected, population size estimated, and subsequently divided into at least 12 identical aliquots of 200,000 worms in ddH2O and flash-frozen in liquid nitrogen and stored at -80°C 8. As a quality control sample, C. elegans IBAT reference material was generated and saved in 200,000 worm aliquots.","SAMPLE_TYPE":"Worms","VOLUMEORAMOUNT_COLLECTED":"200,000 worms","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatments."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen aliquots of 200,000 C. elegans worms were retrieved from -80°C and lyophilized in a VirTis® BenchTop™ “K” Series Freeze Dryer (SP Industries, Inc.). After lyophilization, each aliquot was weighed and stored at -80°C until homogenization. Aliquots were homogenized for three minutes in a Qiagen Tissuelyser 2, using glass beads. Homogenized worms were extracted with 1.5 mL of isopropanol (IPA) at -20°C overnight (approximately 12 hours), then pelleted and the supernatant transferred to separate 2 mL centrifuge tubes. Supernatants were then dried down to completion in a Labconco Centrivap and stored at -80°C for non-polar LC-MS analysis. The pellet was extracted a second time using 80:20 methanol:water (MeOH:H2O) (v:v) for 20 minutes at room temperature (RT) while shaking at 1500 rpm. Samples were again pelleted to separate proteins, and the supernatant was transferred to separate 2 mL centrifuge tubes, dried down to completion, and stored at -80°C for polar LC-MS analysis","SAMPLEPREP_PROTOCOL_FILENAME":"lcms_sequential_extraction_method.pdf","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"IPA for non-polar; 80/20 MeOH/H2O for polar","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"75 µL of IPA containing isotopically labeled lipid standards; 75 µL of 80:20 MeOH: H2O containing isotopically labeled arginine, hypoxanthine, hippuric acid, and methionine"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Non-polar extracts were separated using a Vanquish (ThermoFisher Scientific), fitted with a ThermoFisher Scientific Accucore™ C30 UPLC RP column (2.1 x 150 mm, 2.6 µm particle size). The compounds were eluted with the following gradient: 60:40 acetonitrile:water (ACN:H2O) with 10 mM ammonium formate and 0.1% formic acid (mobile phase A) and 90:10 isopropanol:acetonitrile with 10 mM ammonium formate and 0.1% formic acid (mobile phase B) using the following gradient program: 0.0 min 20% B; 1.0 min 60% B; 5.0 min 70% B; 5.5 min 85% B; 8.0 min 90% B; 8.2-10.5 min 100% B; 10.7-12.0 min 20% B. A curve 5 value was set for 0.0 minutes, and a curve 6 for the remainder of the gradient. The flow rate was set at 0.400 mL min-1. The column temperature was set to 50°C, and the injection volume was 2 µL.","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Scientific Accucore C30 (150 x 2.1mm,2.6um)","COLUMN_TEMPERATURE":"50","SOLVENT_A":"40% water/60% acetonitrile; 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"},

"ANALYSIS":{"LABORATORY_NAME":"Fernandez Lab - Georgia Tech University","ANALYSIS_TYPE":"MS","ACQUISITION_DATE":"7/20/20-7/25/20","OPERATOR_NAME":"Carter Asef","DETECTOR_TYPE":"Orbitrap","DATA_FORMAT":".raw"},

"MS":{"INSTRUMENT_NAME":"Thermo Orbitrap ID-X tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"LC-MS data was collected using a Thermo Orbitrap ID-X tribrid in full profile mode at 240,000 resolution. A m/z range of 150-2000 was used. Data was centroided using Proteowizard and processed using open source software SLAW for peak picking, alignment, and feature assignment.","ION_MODE":"NEGATIVE","CAPILLARY_TEMPERATURE":"275","DRY_GAS_FLOW":"40","DRY_GAS_TEMP":"320","SPRAY_VOLTAGE":"2500","DATAFORMAT":".raw Profile","MS_RESULTS_FILE":"ST002092_AN003417_Results.txt UNITS:Ranked Peak Height  Has m/z:Yes Has RT:Yes RT units:Minutes"}

}