{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000253","ANALYSIS_ID":"AN000401","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics of Neonatal Pulmonary Hypertension (in a Rat Model)","PROJECT_TYPE":"Treatment and feeding study","PROJECT_SUMMARY":"This study aims to identify identify disrupted metabolic pathways and patterns of lung developent in a rat model of bronchopulmonary dysplasia and growth restriction. Pregnant Sprague Dawley rats (gestational day 15) were housed in plsatic cages under constant conditions. After 7-d acclimization period, litters were delivered and pups randomly distributed between litters of 10 pups (N, normal intake) or litters of 17 pups (R, restricted intake). Normal and restriced intake pups were exposed to 75% oxygen (O, oxygen) in a Plexiglass chamber or to 21% oxygen (A, room air) continuously for 14 days, with daily rotation of dams to avoid oxygen toxicity. Both plasma and lung tissue underwent metabolomics analysis.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Department of Pediatrics, School of Medicine","LABORATORY":"Wedgwood lab","LAST_NAME":"Wedgwood","FIRST_NAME":"Stephen","ADDRESS":"1002B, Research II, 4625 2nd Ave., Sacramento, CA 95817","EMAIL":"stephen.wedwood@ucdmc.ucdavis.edu","PHONE":"+1-916-734-1518","FUNDING_SOURCE":"National Institute of Health U24 DK092993","DOI":"http://dx.doi.org/10.21228/M8WK5Q"},

"STUDY":{"STUDY_TITLE":"NIH WCMC Pilot & Feasibility Project: “Metabolomics of Neonatal Pulmonary Hypertension”","STUDY_TYPE":"Treatment and feeding study","STUDY_SUMMARY":"Targeted metabolomic analyses of oxylipins were performed on 16 rat plasma and lung samples collected from rats euthanized at 14 days following exposure to growth restriction and/or hyperoxia. Samples were analyzed by UPLC-MS/MS using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, Framingham, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray ionization.","INSTITUTE":"University of California, Davis","DEPARTMENT":"U.S.D.A. Western Human Nutrition Research Center","LABORATORY":"Newman Lab","LAST_NAME":"Newman","FIRST_NAME":"John","ADDRESS":"430 W. Health Sciences Dr., Davis, CA 95616","EMAIL":"john.newman@ars.usda.gov","PHONE":"+1-530-752-1009","SUBMIT_DATE":"2015-09-03"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Rattus norvegicus","TAXONOMY_ID":"10116","AGE_OR_AGE_RANGE":"2 weeks","ANIMAL_HOUSING":"Litters of 10 (N group) or 17 (R group)","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WEDG-1",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-1.mzML","Osborn ID":"AN1F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-10",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-10.mzML","Osborn ID":"AN3M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-20",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-20.mzML","Osborn ID":"AN2F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-7",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-7.mzML","Osborn ID":"AN4M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-13",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-13.mzML","Osborn ID":"AN1F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-16",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-16.mzML","Osborn ID":"AN4M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-4",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-4.mzML","Osborn ID":"AN2F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-8",
"Factors":{"Treatment":"AN":"Room Air, normal litter (no restricted nutritional intake)","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-8.mzML","Osborn ID":"AN3M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-15",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-15.mzML","Osborn ID":"AR6M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-17",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-17.mzML","Osborn ID":"AR7F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-19",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-19.mzML","Osborn ID":"AR5M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-6",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-6.mzML","Osborn ID":"AR1F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-15",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-15.mzML","Osborn ID":"AR7F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-3",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-3.mzML","Osborn ID":"AR5M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-5",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-5.mzML","Osborn ID":"AR6M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-7",
"Factors":{"Treatment":"AR":"Room Air, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-7.mzML","Osborn ID":"AR1F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-14",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-14.mzML","Osborn ID":"ON6M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-18",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-18.mzML","Osborn ID":"ON4M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-2",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-2.mzML","Osborn ID":"ON7F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-3",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-3.mzML","Osborn ID":"ON8F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-10",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-10.mzML","Osborn ID":"ON4M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-12",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-12.mzML","Osborn ID":"ON7F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-6",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-6.mzML","Osborn ID":"ON8F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-9",
"Factors":{"Treatment":"ON":"75% oxygen, normal litter","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-9.mzML","Osborn ID":"ON6M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-11",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-11.mzML","Osborn ID":"OR9M3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-13",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-13.mzML","Osborn ID":"OR6F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-5",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-5.mzML","Osborn ID":"OR5F3"}
},
{
"Subject ID":"-",
"Sample ID":"WEDG-9",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Lung"},
"Additional sample data":{"Oxylipin analysis":"Wedg Lungs Oxys-WEDG-9.mzML","Osborn ID":"OR4M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-1",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-1.mzML","Osborn ID":"OR5F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-11",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-11.mzML","Osborn ID":"OR9M3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-14",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-14.mzML","Osborn ID":"OR6F3"}
},
{
"Subject ID":"-",
"Sample ID":"PAW-2",
"Factors":{"Treatment":"OR":"75% oxygen, restricted intake","Tissue":"Plasma"},
"Additional sample data":{"Oxylipin analysis":"Osb_Tan_Raj_Oxys-PAW-2.mzML","Osborn ID":"OR4M3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","COLLECTION_PROTOCOL_FILENAME":"NewmanLab-F&BOxys-Protocol-PT.pdf","SAMPLE_TYPE":"Lung and plasma","COLLECTION_METHOD":"Dissection","STORAGE_CONDITIONS":"- 80°C","STORAGE_VIALS":"Eppendorf tubes"},

"TREATMENT":{"TREATMENT_SUMMARY":"Litters of 10 pups (N, normal intake) or litters of 17 pups (R, restricted intake). Normal and restriced intake pups were exposed to 75% oxygen (O, oxygen) in a Plexiglass chamber or to 21% oxygen (A, room air) continuously for 14 days,","TREATMENT_PROTOCOL_FILENAME":"NewmanLab-F&BOxys-Protocol-PT.pdf","TREATMENT":"Intervention","TREATMENT_DOSEDURATION":"1 week","TREATMENT_VEHICLE":"Food availability, oxygen exposure","ANIMAL_ENDP_EUTHANASIA":"2 weeks","ANIMAL_ENDP_TISSUE_COLL_LIST":"Lung and plasma"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Tissues were pulverized on dry ice, enriched with deuterated surrogates, antioxidants (BHT and EDTA), and the total lipid extract was isolated using 10:8:11 cyclohexane/2-propanol/ammonium acetate (v/v/v). Subsequently, esterified oxylipins were liberated via sodium methoxide. Next, the remaining extract was eluted through a Waters Oasis-HLB cartridge. Plasma was added directly to a Waters Ostro plate, mixed with the surrogates, antioxidants, and acetonitrile and the extract eluted through. Both tissue and plasma extracts were dried, reconstituted in 100?L 50:50 methanol:acetonitrile with internal standards 1?phenyl?3?hexanoic acid urea and 1?cyclohexyl?3-dodecanoic acid urea (Sigma-Aldrich, St. Louis, MO) and filtered at 0.1 µm.","SAMPLEPREP_PROTOCOL_FILENAME":"NewmanLab-F&BOxys-Protocol-PT.pdf","EXTRACTION_METHOD":"Liquid:liquid with HLB solid phase extraction (Tissue); Ostro plate (Plasma)","EXTRACT_CLEANUP":"HLB solid phase extraction (Tissue); Ostro plate (Plasma)","EXTRACT_STORAGE":"- 20 °C","SAMPLE_RESUSPENSION":"100 µL","SAMPLE_SPIKING":"See sample prep protocol file","ORGAN":"Lung and plasma"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Oxylipin analysis","METHODS_FILENAME":"NewmanLab-F&BOxys-Protocol-PT.pdf","INSTRUMENT_NAME":"Waters Acquity","COLUMN_TEMPERATURE":"60 C","FLOW_GRADIENT":"See protocol/methods file","FLOW_RATE":"0.25","INTERNAL_STANDARD":"See protocol/methods file","RETENTION_TIME":"See protocol/methods file","SAMPLE_INJECTION":"5 L","SOLVENT_A":"100% water; 0.1% acetic acid","SOLVENT_B":"90% acetonitrile/ 10% isopropanol","ANALYTICAL_TIME":"16 min","WEAK_WASH_SOLVENT_NAME":"20% methanol, 10% isopropanol","WEAK_WASH_VOLUME":"600 L","STRONG_WASH_SOLVENT_NAME":"50:50 Acetonitrile:Methanol","STRONG_WASH_VOLUME":"600 L","SAMPLE_LOOP_SIZE":"17 L"},

"ANALYSIS":{"LABORATORY_NAME":"Newman","ANALYSIS_TYPE":"MS","ANALYSIS_COMMENTS":"Oxylipins analysis - Lung results","ACQUISITION_TIME":"16 min","SOFTWARE_VERSION":"AB Sciex MultiQuant version 3.0.1","OPERATOR_NAME":"Michael La Frano","DETECTOR_TYPE":"API 4000 QTrap (AB Sciex, Framingham, MA, USA)","DATA_FORMAT":".mzML"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex API 4000 QTrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","MS_COMMENTS":"Lung results","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"nM",

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