{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001815","ANALYSIS_ID":"AN002947","VERSION":"1","CREATED_ON":"May 18, 2021, 3:29 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis","PROJECT_TYPE":"Clinical","PROJECT_SUMMARY":"Association of changes in the plasma metabolome with clinical response to methotrexate in children with juvenile idiopathic arthritis.","INSTITUTE":"University Of Kansas","DEPARTMENT":"Pharmacy Practice","LABORATORY":"Funk","LAST_NAME":"Funk","FIRST_NAME":"Ryan","ADDRESS":"2106 Olathe Boulevard, Kansas City, Kansas, 66160, USA","EMAIL":"ryanfunk@kumc.edu","PHONE":"9139456904","FUNDING_SOURCE":"KL2TR002367"},

"STUDY":{"STUDY_TITLE":"Metabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis","STUDY_TYPE":"Clinical","STUDY_SUMMARY":"Plasma from children with juvenile idiopathic arthritis collected pre-treatment and following 3 months of treatment with methotrexate were submitted for metabolomic profiling to the NIH West Coast Metabolomics Center.","INSTITUTE":"University Of Kansas","DEPARTMENT":"Pharmacy Practice","LABORATORY":"Funk Lab","LAST_NAME":"funk","FIRST_NAME":"ryan","ADDRESS":"2106 Olathe Boulevard","EMAIL":"ryanfunk@kumc.edu","PHONE":"9135885000","NUM_GROUPS":"1","TOTAL_SUBJECTS":"30","NUM_MALES":"9","NUM_FEMALES":"21"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"1.8 to 17 years","GENDER":"Not applicable"},
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"COLLECTION":{"COLLECTION_SUMMARY":"Venous blood samples were collected in K2-EDTA containing tubes prior to initiation of MTX and at the patient’s routine 3 month follow up clinic visit along with routine laboratory blood draws. Venous blood samples (10 mL) collected at each timepoint were separated into plasma and cellular fractions by centrifugations at 2,000 RPM in a Beckman tabletop centrifuge for 10 minutes. The resulting supernatant (i.e. plasma fraction) was separated into aliquots and stored at -80 ºC prior to analysis.","SAMPLE_TYPE":"Blood (plasma)","STORAGE_CONDITIONS":"-80℃","ADDITIVES":"K2EDTA"},

"TREATMENT":{"TREATMENT_SUMMARY":"Plasma samples were acquired from a single-center prospective cohort of JIA patients. The study included patients diagnosed with JIA requiring initiation of MTX for inadequately controlled disease without the need for biological therapy at initiation. Diagnosis of JIA was established based on the Edmonton 2001 International League of Associations of Rheumatology (ILAR) criteria for JIA. Patients were initiated on a standardized MTX dose of 15 mg/m2 weekly by subcutaneous or oral administration along with 1 mg folic acid daily. Concurrent medications allowed included nonsteroidal anti-inflammatory drugs (NSAIDs) and daily low-dose steroids (the lesser of 0.2 mg/kg/day or 10 mg). Intra-articular steroid injections (IASI) were allowed, however injected joints were counted as “active” at follow up to reduce the potential bias resulting from IASI.","TREATMENT_COMPOUND":"Methotrexate","TREATMENT_ROUTE":"Oral or Subcutaneous","TREATMENT_DOSE":"15 mg/m^2","TREATMENT_DOSEDURATION":"3 months"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma samples were sent to the West Coast Metabolomics Center and were processed on laboratory Standard Operating Procedures for Sample Preparation of Blood Plasma or Serum Samples for Lipidomic, Biogenic Amine, and Primary Metabolomic Analysis using a biphasic MeOH/MTBE/Water extraction procedure. The upper organic phase was used for lipidomics analysis and the aqueous phase was used for analysis of primary metabolism and biogenic amines."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Lipidomics","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6530","COLUMN_NAME":"Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"Fiehn_laboratory_Lipidomics_CSH_QTOF_lipidomics.pdf"},

"MS":{"INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"MS acquisition, data processing, and feature assignments were conducted at the West Coast Metabolomics Center. Please reference the attached protocols."},

"MS_METABOLITE_DATA":{
"Units":"Peak Height Intensity",

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