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"PROJECT":{"PROJECT_TITLE":"Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis","PROJECT_SUMMARY":"Untargeted NMR study conducted using a NEO 800 MHz Bruker NMR spectrometer where non-polar extracts were collected on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltrasnferase mutants. An augmented design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was performed.","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","FUNDING_SOURCE":"U2CES030167","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 NMR study conducted using a NEO 800 MHz Bruker NMR spectrometer where non-polar extracts were collected on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltrasnferase mutants. An augmented design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was performed.","INSTITUTE":"University of Georgia - Complex Carbohydrate Research Center","LABORATORY":"Edison Lab","LAST_NAME":"Garcia","FIRST_NAME":"Brianna","ADDRESS":"315 Riverbend Road, Athens, GA, 30602, USA","EMAIL":"brianna.garcia@uga.edu","PHONE":"7065424401","NUM_GROUPS":"3","TOTAL_SUBJECTS":"116","STUDY_COMMENTS":"Three study groups of C. elegans strains were used: central metabolism mutants (CMM), UDP-glucuronosyltransferase (UGT) mutants, and natural isolates."},

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"Additional sample data":{"RAW_FILE_NAME":"71","rack_position":"C1","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos82_ga_ms2_75",
"Factors":{"set":"2","batch":"4","genotype":"RB2347"},
"Additional sample data":{"RAW_FILE_NAME":"75","rack_position":"C5","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos83_ga_ms2_117",
"Factors":{"set":"3","batch":"5","genotype":"RB2055"},
"Additional sample data":{"RAW_FILE_NAME":"117","rack_position":"B11","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos84_ga_ms2_76",
"Factors":{"set":"2","batch":"4","genotype":"VC1265"},
"Additional sample data":{"RAW_FILE_NAME":"76","rack_position":"C6","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos85_ga_ms2_140",
"Factors":{"set":"3","batch":"6","genotype":"VC2524"},
"Additional sample data":{"RAW_FILE_NAME":"140","rack_position":"D10","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos85_ga_ms3_98",
"Factors":{"set":"3","batch":"5","genotype":"VC2524"},
"Additional sample data":{"RAW_FILE_NAME":"98","rack_position":"A4","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos86_ga_ms2_65",
"Factors":{"set":"2","batch":"3","genotype":"KJ550"},
"Additional sample data":{"RAW_FILE_NAME":"65","rack_position":"B7","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos87_co_ms3_72",
"Factors":{"set":"2","batch":"4","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"72","rack_position":"C2","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos87_ga_ms3_118",
"Factors":{"set":"3","batch":"5","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"118","rack_position":"B12","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos88_ga_ms2_138",
"Factors":{"set":"3","batch":"6","genotype":"UGT49"},
"Additional sample data":{"RAW_FILE_NAME":"138","rack_position":"D8","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos90_ga_ms3_66",
"Factors":{"set":"2","batch":"3","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"66","rack_position":"B8","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos91_ga_ms2_119",
"Factors":{"set":"3","batch":"5","genotype":"AUM2073"},
"Additional sample data":{"RAW_FILE_NAME":"119","rack_position":"C1","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos92_ga_ms2_77",
"Factors":{"set":"2","batch":"4","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"77","rack_position":"C7","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos93_ga_ms2_78",
"Factors":{"set":"2","batch":"4","genotype":"VC1265"},
"Additional sample data":{"RAW_FILE_NAME":"78","rack_position":"C8","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos94_ga_ms2_139",
"Factors":{"set":"3","batch":"6","genotype":"VC2524"},
"Additional sample data":{"RAW_FILE_NAME":"139","rack_position":"D9","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos95_ga_ms2_79",
"Factors":{"set":"2","batch":"4","genotype":"RB2347"},
"Additional sample data":{"RAW_FILE_NAME":"79","rack_position":"C9","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos96_ga_ms2_74",
"Factors":{"set":"2","batch":"4","genotype":"RB2550"},
"Additional sample data":{"RAW_FILE_NAME":"74","rack_position":"C4","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos98_ga_ms2_67",
"Factors":{"set":"2","batch":"3","genotype":"VC1265"},
"Additional sample data":{"RAW_FILE_NAME":"67","rack_position":"B9","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos99_ga_ms2_141",
"Factors":{"set":"3","batch":"6","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"141","rack_position":"D11","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos99_ga_ms2_26",
"Factors":{"set":"1","batch":"2","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"26","rack_position":"C2","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"aos99_ga_ms2_68",
"Factors":{"set":"2","batch":"3","genotype":"PD1074"},
"Additional sample data":{"RAW_FILE_NAME":"68","rack_position":"B10","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_mutant_142",
"Factors":{"set":"3","batch":"6","genotype":"pooled_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"142","rack_position":"D12","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_mutant_90",
"Factors":{"set":"2","batch":"4","genotype":"pooled_mutant"},
"Additional sample data":{"RAW_FILE_NAME":"90","rack_position":"D8","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_natural_isolate_42",
"Factors":{"set":"1","batch":"2","genotype":"pooled_natural_isolate"},
"Additional sample data":{"RAW_FILE_NAME":"42","rack_position":"D6","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_pd1074_143",
"Factors":{"set":"3","batch":"6","genotype":"pooled_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"143","rack_position":"E1","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_pd1074_43",
"Factors":{"set":"1","batch":"2","genotype":"pooled_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"43","rack_position":"D7","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"pooled_pd1074_91",
"Factors":{"set":"2","batch":"4","genotype":"pooled_pd1074"},
"Additional sample data":{"RAW_FILE_NAME":"91","rack_position":"D9","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_144",
"Factors":{"set":"3","batch":"6","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"144","rack_position":"E2","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_3",
"Factors":{"set":"1","batch":"1","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"3","rack_position":"A3","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_44",
"Factors":{"set":"1","batch":"2","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"44","rack_position":"D8","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_49",
"Factors":{"set":"2","batch":"3","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"49","rack_position":"A3","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_92",
"Factors":{"set":"2","batch":"4","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"92","rack_position":"D10","parameters":"proton"}
},
{
"Subject ID":"-",
"Sample ID":"solera_97",
"Factors":{"set":"3","batch":"5","genotype":"solera"},
"Additional sample data":{"RAW_FILE_NAME":"97","rack_position":"A3","parameters":"proton"}
}
],
"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. 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 lyophilized C. elegans aliquots were retrieved from -80°C. 200 μL of 1 mm zirconia beads were added to each sample and homogenized at 420 rcf for 90 seconds in a FastPrep-96 homogenizer and subsequently placed on dry ice for 90 seconds to avoid overheating, this step was repeated twice for a total of three rounds. Using the homogenized samples, 1 mL of 100% IPA chilled to -20°C was added to the lyophilized/homogenized sample powder and Zirconia beads in two increments of 500 μL. After each addition of 500 μL, samples were vortexed for 30 seconds – 1 minute and left at RT for 15 - 20 minutes. After RT incubation, samples were stored overnight (~12 hours) at -20°C. Samples were centrifuged for 30 minutes at 4°C (20,800 rcf). The supernatant was transferred to a new tube to use for analysis of non-polar molecules. 1 mL of pre-chilled 80:20 MeOH:H2O (4°C) was added to the remaining worm pellet to analyze polar molecules. The polar fraction shook at 4°C for 30 minutes. Samples were centrifuged at 20,800 rcf for 30 minutes at 4°C. The supernatant was transferred to a new tube to use for analysis of non-polar molecules. Both polar and non-polar samples were placed in a Labconco Centrivap at RT and monitored until completely dry. Once dry, polar and non-polar samples were reconstituted in D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) and CDCl3 (99.96%, Cambridge Isotope Laboratories, Inc.) respectively. Samples were vortexed until fully soluble, and 45 μL of each sample were transferred into 1.7 mm NMR tubes (Bruker SampleJet) for acquisition.","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"Sequential extraction of (1) IPA for non-polar molecule followed by (2) 80/20 MeOH/H2O for polar","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"CDCl3 for non-polar; D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) for polar"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","LABORATORY_NAME":"Edison Lab – Complex Carbohydrate Research Center","OPERATOR_NAME":"Amanda O. Shaver","DETECTOR_TYPE":"Bruker Neo 1.7 mm TCI Cryo Probe","ACQUISITION_DATE":"2020-03-30","DATA_FORMAT":"ft"},

"NM":{"INSTRUMENT_NAME":"Bruker Neo 800 MHz","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"800","NMR_PROBE":"1.7 mm TCI cryoprobe","NMR_SOLVENT":"CDCl3","NMR_TUBE_SIZE":"1.7 mm","SHIMMING_METHOD":"Automatic (“Topshim”)","PULSE_SEQUENCE":"zg","WATER_SUPPRESSION":"3758.64 @ 4.7 ppm","RECEIVER_GAIN":"65.1","TEMPERATURE":"6","NUMBER_OF_SCANS":"64","DUMMY_SCANS":"4","ACQUISITION_TIME":"1.31 sec","SPECTRAL_WIDTH":"20.2","NUM_DATA_POINTS_ACQUIRED":"65,536","LINE_BROADENING":"1.5","APODIZATION":"exponential","BASELINE_CORRECTION_METHOD":"Polynomial Automatic fit","CHEMICAL_SHIFT_REF_STD":"7.24","NMR_RESULTS_FILE":"ST002096_AN003424_Results.txt UNITS:Ranked Intensity"}

}