{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000515","ANALYSIS_ID":"AN000789","VERSION":"1","CREATED_ON":"December 12, 2016, 1:48 pm"},

"PROJECT":{"PROJECT_TITLE":"The Malaria Host-Pathogen Interaction Center (MaHPIC)","PROJECT_TYPE":"Systems Biology","PROJECT_SUMMARY":"The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program supported by an NIH/NIAID contract (# HHSN272201200031C; see http://www.systemsbiology.emory.edu/index.html). The MaHPIC generates many data types (e.g., metabolomics, functional genomics, lipidomics, proteomics, clinical, parasitological, immune response) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates, and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC: Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director), and Ebru Karpuzoglu ekarpuzoglu@emory.edu  (MaHPIC Scientific Project Manager)","INSTITUTE":"Emory University","DEPARTMENT":"School of Medicine, Vaccine Center at Yerkes","LAST_NAME":"Galinski","FIRST_NAME":"Mary","ADDRESS":"Emory University, 954 Gatewood Rd, Room 208, Atlanta, GA 30329","EMAIL":"mgalins@emory.edu","PHONE":"N/A","FUNDING_SOURCE":"NIAID Contract: # HHSN272201200031C"},

"STUDY":{"STUDY_TITLE":"Metabolomics of longitudinal plasma samples from Macaca mulatta infected with Plasmodium cynomolgi B strain.","STUDY_TYPE":"Longitudinal parasite infection and treatment of multiple individuals","STUDY_SUMMARY":"Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug Artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs Primaquine and Chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and during seven-time point collections of venous blood. Supplemental files, including a ReadMe with additional experimental details, all raw data, and analytical metadata, are provided as part of this submission.","INSTITUTE":"Emory University","DEPARTMENT":"School of Medicine, Vaccine Center at Yerkes","LAST_NAME":"Karpuzoglu","FIRST_NAME":"Ebru","ADDRESS":"Emory University, 954 Gatewood Rd, Room 208, Atlanta, GA 30329","EMAIL":"mahpic@emory.edu","PHONE":"N/A","TOTAL_SUBJECTS":"5","STUDY_COMMENTS":"Malaria Host Pathogen Interaction Center Experiment 04, 5 subjects 286 samples, The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04). To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public."},

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"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"-1"},
"Additional sample data":{"Collection Type":"Time Point 1"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1979561",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"1"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1981043",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"3"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1981187",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"5"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1985073",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"7"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1985568",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"9"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1986962",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"11"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1988265",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"13"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1990916",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"15"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1991841",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"17"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1993046",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"19"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1995922",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"21"},
"Additional sample data":{"Collection Type":"Time Point 2"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1998668",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"23"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1999129",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"25"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"1999443",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"26"},
"Additional sample data":{"Collection Type":"Time Point 3"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2003641",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"27"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2005646",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"29"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2005905",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"31"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2006389",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"33"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2008343",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"35"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2010130",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"37"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2010689",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"39"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2012642",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"41"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2013482",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"43"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2014519",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"45"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2016524",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"47"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2018670",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"49"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2018946",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"51"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2019942",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"53"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2021458",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"55"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2023633",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"57"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2023653",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"59"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2024650",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"61"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2026410",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"63"},
"Additional sample data":{"Collection Type":"Time Point 4"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2028718",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"65"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2029130",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"67"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2030951",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"69"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2033040",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"71"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2033076",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"73"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2034626",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"75"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2030290",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"76"},
"Additional sample data":{"Collection Type":"Time Point 5"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2036397",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"77"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2034994",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"79"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2042765",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"81"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2044196",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"83"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2043811",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"85"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2044232",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"87"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2046022",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"89"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2045897",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"91"},
"Additional sample data":{"Collection Type":"Time Point 6"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2046335",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"93"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2050232",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"95"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2050765",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"97"},
"Additional sample data":{"Collection Type":"Time Point 7"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2055194",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"99"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2058603",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"104"},
"Additional sample data":{"Collection Type":"Every Other Day"}
},
{
"Subject ID":"RSb14",
"Sample ID":"2060797",
"Factors":{"Gender":"Male","Prior Infection":"None","Days since Inoculation":"106"},
"Additional sample data":{"Collection Type":"Every Other Day"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Every Other Day Collection|Time Point 1 - Baseline: Uninfected control for each NHP.|Time Point 2 - Peak of infection: Peak of infection determined by clinical and parasitological assessment for each NHP. The time point is intended to characterize the host immune response and capture multi-omics data during the peak of parasitemias when the NHP is experiencing clinical signs of disease that may be severe or non-severe. NHPs were monitored, and clinical interventions were performed as necessary. Otherwise, NHPs self-resolved infection.|Time Point 3 - Post-Peak of Infection: Observations 7 days after peak infection.|Time Point 4 - 1st Relapse Peak of Infection: This time point tested expectations of a mild drop in hemoglobin levels and low parasitemias relative to peak infection arising from activation of hypnozoites. |Time Point 5 - Post-Peak of 1st Relapse Infection: Inter-relapse interval. |Time Point 6 - 2nd Relapse Peak of Infection: Same goal as time point 4 for 2nd relapse.|Time Point 7 - Post-Peak of 2nd Relapse Infection: Observations on NHP response after a second relapse infection.","SAMPLE_TYPE":"Whole blood","COLLECTION_METHOD":"Ear Prick|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous","COLLECTION_TIME":"Every Other Day|Once|Once|Once|Once|Once|Once|Once","BLOOD_SERUM_OR_PLASMA":"Plasma"},

"TREATMENT":{"TREATMENT_SUMMARY":"Plasmodium Cynomolgi Strain B Sporozoites Inoculation","TREATMENT":"Biotic","TREATMENT_ROUTE":"Injection"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"aliquots of 65ul sample were mixed with 130ul acetonitrile and 3.25ul internal standard. Keep on ice and vortex every 15 minutes. Centrifuge for 10 minutes at 13.2rpm and 4C. Using a pipette, 130ul of supernatant was removed and placed into autosampler vials for the mass spectrometer.","SAMPLEPREP_PROTOCOL_FILENAME":"Metab_Sample_Preparation_Plasma_serum_v1_May_17_2013.docx;E4_E3_E18_E23_E24_E25_MalariaCore_Metabolomics SOP_v1_6October2016.docx","PROCESSING_METHOD":"Precipitation of protein, centrifuge, and remove supernatant","PROCESSING_STORAGE_CONDITIONS":"on ice","EXTRACTION_METHOD":"1:2 sample:acetonitrile","EXTRACT_STORAGE":"Pipette supernatant into autosampler vials for mass spectrometer","SAMPLE_SPIKING":"C18 standards: Caffeine and Diethyl-toluamide. Stable isotopes: [13C6]-D-glucose, [15N]-indole, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [15N]-choline chloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,4-13C2]-cholesterol, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"untargeted chromatography (C18 column)","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo QExactive","COLUMN_NAME":"Higgins C18 100x2.1mm, 5um","FLOW_GRADIENT":"A%: 0-10mins = 5%; B%: 0-2mins = 35%, 2-7mins = gradient to 95%, 7-10mins = 95%; C%: 0-2mins = 60%, 2-7mins = gradient to 0%, 7-10mins = 0%","FLOW_RATE":"0-2mins = 350 μL/min, 2-7mins = gradient to 400 μL/min, 7-10mins = 400 μL/min","COLUMN_TEMPERATURE":"30","SOLVENT_A":"LC grade H2O with 2% Formic Acid","SOLVENT_B":"Acetonitrile (LC grade)","COLUMN_PRESSURE":"200 Bar (max)","INJECTION_TEMPERATURE":"4C","INTERNAL_STANDARD":"Caffeine, Diethyl-toluamide","INTERNAL_STANDARD_MT":"1.5 min; 6-6.6 min","SAMPLE_INJECTION":"10μL","SAMPLING_CONE":"ESI: HESI probe with S-lens combination","ANALYTICAL_TIME":"10 minutes","CAPILLARY_VOLTAGE":"4.6 kV","OVEN_TEMPERATURE":"45C","RUNNING_VOLTAGE":"4.6 kV","CHROMATOGRAPHY_COMMENTS":"Thermo QExactive coupled to CTC PAL HTC Accela1-TMO autosampler"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","CAPILLARY_TEMPERATURE":"250","CAPILLARY_VOLTAGE":"4.45","COLLISION_GAS":"N2","GAS_PRESSURE":"50 PSI","IONIZATION":"electrospray ionization","MASS_ACCURACY":"5 PPM","SOURCE_TEMPERATURE":"48","SPRAY_VOLTAGE":"3.5","ATOM_GUN_CURRENT":"1000000","DATAFORMAT":".raw,.cdf","PROBE_TIP":"HESI","RESOLUTION_SETTING":"120,000","SCAN_RANGE_MOVERZ":"85-1275"},

"MS_METABOLITE_DATA":{
"Units":"peak intensity",

"Data":[],

"Metabolites":[]
}

}