{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000100","ANALYSIS_ID":"AN000165","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Global Metabolomics of C. elegans using an augmented reference IROA design","PROJECT_SUMMARY":"-","INSTITUTE":"University of Florida","DEPARTMENT":"Biochemistry & Molecular Biology","LAST_NAME":"Edison","FIRST_NAME":"Arthur","ADDRESS":"R3-226 Academic Research Building, Department of Biochemistry & Molecular PO Box 100245, Gainesville, Fl","EMAIL":"aedison@ufl.edu","PHONE":"(352) 392-4535","FUNDING_SOURCE":"NIH"},

"STUDY":{"STUDY_TITLE":"Global Metabolomics of C. elegans using an augmented reference IROA design","STUDY_TYPE":"heat shock","STUDY_SUMMARY":"Global Metabolomics of C. elegans using an augmented reference IROA design","INSTITUTE":"University of Florida","DEPARTMENT":"Biochemistry & Molecular Biology","LABORATORY":"Arthur Edison","LAST_NAME":"Edison","FIRST_NAME":"Arthur","ADDRESS":"R3-226 Academic Research Building, Department of Biochemistry & Molecular PO Box 100245, Gainesville, FL 32610-0245","EMAIL":"aedison@ufl.edu","PHONE":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Caenorhabditis elegans","TAXONOMY_ID":"6329","GENOTYPE_STRAIN":"N2","AGE_OR_AGE_RANGE":"Young adult","GENDER":"Hermaphrodite","SPECIES_GROUP":"Invertebrate"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Worm",
"Sample ID":"10PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"10","ExperRep":"1,2","PairID":"101,102","SampleID":"37,38","SampleOrder":"32,48"}
},
{
"Subject ID":"Worm",
"Sample ID":"11PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"11","ExperRep":"1,2","PairID":"111,112","SampleID":"41,42","SampleOrder":"8,2"}
},
{
"Subject ID":"Worm",
"Sample ID":"12PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"12","ExperRep":"1,2","PairID":"121,122","SampleID":"45,46","SampleOrder":"23,33"}
},
{
"Subject ID":"Worm",
"Sample ID":"1PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"1","ExperRep":"1,2","PairID":"11,12","SampleID":"1,2","SampleOrder":"19,35"}
},
{
"Subject ID":"Worm",
"Sample ID":"2PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"2","ExperRep":"1,2","PairID":"21,22","SampleID":"5,6","SampleOrder":"40,37"}
},
{
"Subject ID":"Worm",
"Sample ID":"3PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"3","ExperRep":"1,2","PairID":"31,32","SampleID":"9,10","SampleOrder":"25,12"}
},
{
"Subject ID":"Worm",
"Sample ID":"4PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"4","ExperRep":"1,2","PairID":"41,42","SampleID":"13,14","SampleOrder":"10,6"}
},
{
"Subject ID":"Worm",
"Sample ID":"5PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"5","ExperRep":"1,2","PairID":"51,52","SampleID":"17,18","SampleOrder":"22,45"}
},
{
"Subject ID":"Worm",
"Sample ID":"6PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"6","ExperRep":"1,2","PairID":"61,62","SampleID":"21,22","SampleOrder":"15,44"}
},
{
"Subject ID":"Worm",
"Sample ID":"7PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"7","ExperRep":"1,2","PairID":"71,72","SampleID":"25,26","SampleOrder":"41,4"}
},
{
"Subject ID":"Worm",
"Sample ID":"8PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"8","ExperRep":"1,2","PairID":"81,82","SampleID":"29,30","SampleOrder":"17,13"}
},
{
"Subject ID":"Worm",
"Sample ID":"9PC-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"9","ExperRep":"1,2","PairID":"91,92","SampleID":"33,34","SampleOrder":"27,30"}
},
{
"Subject ID":"Worm",
"Sample ID":"10PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"10","ExperRep":"1,2","PairID":"101,102","SampleID":"39,40","SampleOrder":"31,47"}
},
{
"Subject ID":"Worm",
"Sample ID":"11PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"11","ExperRep":"1,2","PairID":"111,112","SampleID":"43,44","SampleOrder":"7,1"}
},
{
"Subject ID":"Worm",
"Sample ID":"12PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"12","ExperRep":"1,2","PairID":"121,122","SampleID":"47,48","SampleOrder":"24,34"}
},
{
"Subject ID":"Worm",
"Sample ID":"1PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"1","ExperRep":"1,2","PairID":"11,12","SampleID":"3,4","SampleOrder":"20,36"}
},
{
"Subject ID":"Worm",
"Sample ID":"2PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"2","ExperRep":"1,2","PairID":"21,22","SampleID":"7,8","SampleOrder":"39,38"}
},
{
"Subject ID":"Worm",
"Sample ID":"3PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"3","ExperRep":"1,2","PairID":"31,32","SampleID":"11,12","SampleOrder":"26,11"}
},
{
"Subject ID":"Worm",
"Sample ID":"4PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"4","ExperRep":"1,2","PairID":"41,42","SampleID":"15,16","SampleOrder":"9,5"}
},
{
"Subject ID":"Worm",
"Sample ID":"5PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"5","ExperRep":"1,2","PairID":"51,52","SampleID":"19,20","SampleOrder":"21,46"}
},
{
"Subject ID":"Worm",
"Sample ID":"6PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"6","ExperRep":"1,2","PairID":"61,62","SampleID":"23,24","SampleOrder":"16,43"}
},
{
"Subject ID":"Worm",
"Sample ID":"7PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"7","ExperRep":"1,2","PairID":"71,72","SampleID":"27,28","SampleOrder":"42,3"}
},
{
"Subject ID":"Worm",
"Sample ID":"8PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"8","ExperRep":"1,2","PairID":"81,82","SampleID":"31,32","SampleOrder":"18,14"}
},
{
"Subject ID":"Worm",
"Sample ID":"9PHS-5",
"Factors":{"Labelling":"0.05","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"9","ExperRep":"1,2","PairID":"91,92","SampleID":"35,36","SampleOrder":"28,29"}
},
{
"Subject ID":"Worm",
"Sample ID":"10PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"10","ExperRep":"1,2","PairID":"101,102","SampleID":"37,38","SampleOrder":"32,48"}
},
{
"Subject ID":"Worm",
"Sample ID":"11PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"11","ExperRep":"1,2","PairID":"111,112","SampleID":"41,42","SampleOrder":"8,2"}
},
{
"Subject ID":"Worm",
"Sample ID":"12PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"12","ExperRep":"1,2","PairID":"121,122","SampleID":"45,46","SampleOrder":"23,33"}
},
{
"Subject ID":"Worm",
"Sample ID":"1PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"1","ExperRep":"1,2","PairID":"11,12","SampleID":"1,2","SampleOrder":"19,35"}
},
{
"Subject ID":"Worm",
"Sample ID":"2PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"2","ExperRep":"1,2","PairID":"21,22","SampleID":"5,6","SampleOrder":"40,37"}
},
{
"Subject ID":"Worm",
"Sample ID":"3PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"3","ExperRep":"1,2","PairID":"31,32","SampleID":"9,10","SampleOrder":"25,12"}
},
{
"Subject ID":"Worm",
"Sample ID":"4PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"4","ExperRep":"1,2","PairID":"41,42","SampleID":"13,14","SampleOrder":"10,6"}
},
{
"Subject ID":"Worm",
"Sample ID":"5PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"5","ExperRep":"1,2","PairID":"51,52","SampleID":"17,18","SampleOrder":"22,45"}
},
{
"Subject ID":"Worm",
"Sample ID":"6PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"6","ExperRep":"1,2","PairID":"61,62","SampleID":"21,22","SampleOrder":"15,44"}
},
{
"Subject ID":"Worm",
"Sample ID":"7PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"7","ExperRep":"1,2","PairID":"71,72","SampleID":"25,26","SampleOrder":"41,4"}
},
{
"Subject ID":"Worm",
"Sample ID":"8PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"8","ExperRep":"1,2","PairID":"81,82","SampleID":"29,30","SampleOrder":"17,13"}
},
{
"Subject ID":"Worm",
"Sample ID":"9PC-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"9","ExperRep":"1,2","PairID":"91,92","SampleID":"33,34","SampleOrder":"27,30"}
},
{
"Subject ID":"Worm",
"Sample ID":"10PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"10","ExperRep":"1,2","PairID":"101,102","SampleID":"39,40","SampleOrder":"31,47"}
},
{
"Subject ID":"Worm",
"Sample ID":"11PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"11","ExperRep":"1,2","PairID":"111,112","SampleID":"43,44","SampleOrder":"7,1"}
},
{
"Subject ID":"Worm",
"Sample ID":"12PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"4","BioRep":"12","ExperRep":"1,2","PairID":"121,122","SampleID":"47,58","SampleOrder":"24,34"}
},
{
"Subject ID":"Worm",
"Sample ID":"1PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"1","ExperRep":"1,2","PairID":"11,12","SampleID":"3,4","SampleOrder":"20,36"}
},
{
"Subject ID":"Worm",
"Sample ID":"2PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"2","ExperRep":"1,2","PairID":"21,22","SampleID":"7,8","SampleOrder":"39,38"}
},
{
"Subject ID":"Worm",
"Sample ID":"3PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"1","BioRep":"3","ExperRep":"1,2","PairID":"31,32","SampleID":"11,12","SampleOrder":"26,11"}
},
{
"Subject ID":"Worm",
"Sample ID":"4PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"4","ExperRep":"1,2","PairID":"41,42","SampleID":"15,16","SampleOrder":"9,5"}
},
{
"Subject ID":"Worm",
"Sample ID":"5PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"5","ExperRep":"1,2","PairID":"51,52","SampleID":"19,20","SampleOrder":"21,46"}
},
{
"Subject ID":"Worm",
"Sample ID":"6PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"2","BioRep":"6","ExperRep":"1,2","PairID":"61,62","SampleID":"23,24","SampleOrder":"16,43"}
},
{
"Subject ID":"Worm",
"Sample ID":"7PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"7","ExperRep":"1,2","PairID":"71,72","SampleID":"27,28","SampleOrder":"42,3"}
},
{
"Subject ID":"Worm",
"Sample ID":"8PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"8","ExperRep":"1,2","PairID":"81,82","SampleID":"31,32","SampleOrder":"18,14"}
},
{
"Subject ID":"Worm",
"Sample ID":"9PHS-95",
"Factors":{"Labelling":"0.95","Experimentalgroup":"no heat-shock"},
"Additional sample data":{"Batch":"3","BioRep":"9","ExperRep":"1,2","PairID":"91,92","SampleID":"35,36","SampleOrder":"28,29"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Each flask was separated into supernatant (exometabolome) and worm pellet by centrifugation 2,000 rpm for 2 min.","COLLECTION_PROTOCOL_ID":"Centrifugation","COLLECTION_PROTOCOL_FILENAME":"Experimental_Methods.docx","VOLUMEORAMOUNT_COLLECTED":"25,000 worms in 2.5 mL"},

"TREATMENT":{"TREATMENT_SUMMARY":"Samples were treated with a 20 min heat shock at 33 °C followed by incubation 22C for 100 min. Sample shook at 250 rpm at a worm density of 10,000 worms per Samples were incubated at 22C for 120 min. Sample shook at 250 rpm at a worm of 10,000 worms per mL.","TREATMENT_PROTOCOL_ID":"Test/Control"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_ID":"Endometabolome","SAMPLEPREP_PROTOCOL_FILENAME":"Experimental_Methods.docx","SAMPLEPREP_PROTOCOL_COMMENTS":"The worm pellets were homogenized using a FastPrep-24 (MP Biomedicals) using Matrix E tubes for 5 cycles of 60 sec in 80% methanol and then frozen at -80","PROCESSING_METHOD":"Homogenization"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples were analyzed using a mass range of m/z 70-1000 in positive and ionization mode, externally calibrated, using a Thermo Scientific Q-Exactive mass spectrometer equipped with a Dionex UltiMate 3000 RS autosampler and pump. ?L of each sample were injected onto an Acquity UPLC HSS T3 (2.1x100 mm, 1.8 column using a column temperature of 35 C and a flow rate of 300 L/min with A (0.1% formic acid in water (Fisher LC-MS Optima)) held at 100% A for 1 min, by linear increase to 80% B (0.1% formic acid in acetonitrile) over 10 min, constant for 2 min, followed by a return to initial conditions over 0.5 min and for 3 min.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","COLUMN_NAME":"Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)","FLOW_GRADIENT":"A held at 100% A for 1 min, followed by linear increase to 80% B over 10 min, constant for 2 min, followed by a return to initial conditions over 0.5 min and for 3 min","FLOW_RATE":"300 L/min","SAMPLE_INJECTION":"3 ?L","SOLVENT_A":"0.1% formic acid in water (Fisher LC-MS Optima)","SOLVENT_B":"0.1% formic acid in acetonitrile"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Edison","OPERATOR_NAME":"Chaevien Clendinen","DETECTOR_TYPE":"Positive"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"The Q-Exactive was equipped with a Heated Electrospray Ionization (HESI) source operated at a spray temperature of 350 ?C, a spray voltage of 3.5 kV, and and auxiliary gas flow rates of 50 and 10 arbitrary units, respectively. The temperature was held at 325 ?C, and the S-lens RF Level was set to 40%. The FR was set to 70,000 at m/z 200. The accuracy achieved was routinely less than 1.5","CAPILLARY_TEMPERATURE":"325 ?C","ION_SOURCE_TEMPERATURE":"350 ?C","ION_SPRAY_VOLTAGE":"3.5 kV","RESOLUTION_SETTING":"70000"}

}