{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000592","ANALYSIS_ID":"AN000907","VERSION":"1","CREATED_ON":"April 17, 2017, 10:07 am"},

"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). The MaHPIC generates many data types (e.g., clinical, parasitological, metabolomics, functional genomics, lipidomics, proteomics, 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.","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":"mahpic@emory.edu","PHONE":"none","FUNDING_SOURCE":"NIAID Contract: # HHSN272201200031C"},

"STUDY":{"STUDY_TITLE":"Experiment 13: Uninfected Macaca mulatta exposed to pyrimethamine to produce and integrate clinical, hematological, and omics control measures.","STUDY_SUMMARY":"Uninfected, malaria-naive, male rhesus macaques (Macaca mulatta), approximately two years of age, were inoculated intravenously with a preparation of salivary gland material derived from non-infected Anopheles dirus and profiled for clinical, hematological, functional genomic, lipidomic, proteomic, and metabolomic measurements. Samples were generated and analyzed to investigate the effects of the pharmacological intervention with the anti-malarial drug pyrimethamine on normal individuals. The experiment was designed for 100 days plus a follow-up period, with pyrimethamine administered at three different time points to coincide with the predicted treatment days of experimentally infected rhesus macaques. Capillary blood samples were collected daily for the measurement of CBCs and reticulocytes. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples and bone marrow aspirates were collected at seven time points before and after three rounds of drug administration for functional genomic, proteomic, and lipidomic analyses. Within the MaHPIC, this project is known as 'Experiment 13'. This dataset was produced by Dean Jones at Emory University. The following contributed to the creation of this dataset: The MaHPIC Consortium, John Barnwell, Monica Cabrera, Jeremy D. DeBarry, Mary Galinski, Trenton Hoffman, Jay Humphrey, Jianlin Jiang, Chet Joyner, Nicolas Lackman, Stacey Lapp, Esmeralda Meyer, Alberto Moreno, Mustafa Nural, and Suman Pakala. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).","INSTITUTE":"Emory University","DEPARTMENT":"School of Medicine, Vaccine Center at Yerkes","LAST_NAME":"Galinksi","FIRST_NAME":"Mary","ADDRESS":"Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329","EMAIL":"mahpic@emory.edu","PHONE":"none","TOTAL_SUBJECTS":"6","STUDY_COMMENTS":"31 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 13' (E13). To access other publicly available results from E13 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. See Pubmed ID:25453034 for the associated publication for this study."},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Macaca mulatta","TAXONOMY_ID":"9544","GENOTYPE_STRAIN":"N/A|6.53kg|6.87kg|6.09kg|7.23kg|6.48kg","GENDER":"Male| Male| Male| Male| Male| Male","ANIMAL_ANIMAL_SUPPLIER":"none|Yerkes Field Station|Yerkes Primate Research Center|Yerkes Primate Research Center| |Yerkes Primate Research Center","ANIMAL_HOUSING":"Metallic|Metallic|Metallic|Metallic|Metallic|Metallic","ANIMAL_LIGHT_CYCLE":"12/11|12/12|12/12|12/12|12/12|12/12","ANIMAL_FEED":"Monkey Jumbo Diet 5037 and 5038","ANIMAL_WATER":"tap in bottle","ANIMAL_INCLUSION_CRITERIA":"Weight"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"RCs13",
"Sample ID":"1906030",
"Factors":{"Collection Type":"Time Point 3"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RCs13",
"Sample ID":"1932199",
"Factors":{"Collection Type":"Time Point 4"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RCs13",
"Sample ID":"1941204",
"Factors":{"Collection Type":"Time Point 5"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RCs13",
"Sample ID":"1968402",
"Factors":{"Collection Type":"Time Point 6"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RCs13",
"Sample ID":"1972662",
"Factors":{"Collection Type":"Time Point 7"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"REe6",
"Sample ID":"1892525",
"Factors":{"Collection Type":"Reference"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RTi13",
"Sample ID":"1906044",
"Factors":{"Collection Type":"Time Point 3"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RTi13",
"Sample ID":"1932200",
"Factors":{"Collection Type":"Time Point 4"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RTi13",
"Sample ID":"1941205",
"Factors":{"Collection Type":"Time Point 5"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RTi13",
"Sample ID":"1968432",
"Factors":{"Collection Type":"Time Point 6"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RTi13",
"Sample ID":"1972668",
"Factors":{"Collection Type":"Time Point 7"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RUn13",
"Sample ID":"1906045",
"Factors":{"Collection Type":"Time Point 3"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RUn13",
"Sample ID":"1932201",
"Factors":{"Collection Type":"Time Point 4"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RUn13",
"Sample ID":"1941206",
"Factors":{"Collection Type":"Time Point 5"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RUn13",
"Sample ID":"1968433",
"Factors":{"Collection Type":"Time Point 6"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RUn13",
"Sample ID":"1972674",
"Factors":{"Collection Type":"Time Point 7"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RWr13",
"Sample ID":"1906046",
"Factors":{"Collection Type":"Time Point 3"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RWr13",
"Sample ID":"1932202",
"Factors":{"Collection Type":"Time Point 4"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RWr13",
"Sample ID":"1941207",
"Factors":{"Collection Type":"Time Point 5"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RWr13",
"Sample ID":"1968434",
"Factors":{"Collection Type":"Time Point 6"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RWr13",
"Sample ID":"1972680",
"Factors":{"Collection Type":"Time Point 7"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RZe13",
"Sample ID":"1906047",
"Factors":{"Collection Type":"Time Point 3"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RZe13",
"Sample ID":"1932203",
"Factors":{"Collection Type":"Time Point 4"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RZe13",
"Sample ID":"1941208",
"Factors":{"Collection Type":"Time Point 5"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RZe13",
"Sample ID":"1968435",
"Factors":{"Collection Type":"Time Point 6"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"RZe13",
"Sample ID":"1972686",
"Factors":{"Collection Type":"Time Point 7"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"N/A",
"Sample ID":"9991200135",
"Factors":{"Collection Type":"QC Sample, in-lab prepared"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"N/A",
"Sample ID":"9991200136",
"Factors":{"Collection Type":"QC Sample, in-lab prepared"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"N/A",
"Sample ID":"9991100046",
"Factors":{"Collection Type":"QC Sample, from NIST"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"N/A",
"Sample ID":"9991200137",
"Factors":{"Collection Type":"QC Sample, in-lab prepared"},
"Additional sample data":{"Gender":"Male"}
},
{
"Subject ID":"N/A",
"Sample ID":"9991100047",
"Factors":{"Collection Type":"QC Sample, from NIST"},
"Additional sample data":{"Gender":"Male"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Time Point 3 Post-Rx: Observations on NHP response six days after administration of Pyrimethamine|Time Point 4 Rx: Pyrimethamine was administered at 1 mg/kg/day IM for three days|Time Point 5 Post-Rx: Observations on NHP response seven days after initiation of the anti-malarial regimen|Time Point 6 Rx: Pyrimethamine was administered at 1 mg/kg/day IM for three days|Time Point 7 Post-Rx: Observations on NHP response eight days after initiation of the anti-malarial regimen","SAMPLE_TYPE":"Whole blood","COLLECTION_METHOD":"Intravenous","COLLECTION_FREQUENCY":"once","BLOOD_SERUM_OR_PLASMA":"Plasma"},

"TREATMENT":{"TREATMENT_SUMMARY":"None"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"aliquots of 65ul sample were mixed with 130ul acetonitrile and 3.25ul internal standard. Keep on ice for 30 minutes 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","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. Anion Exchange Standards: Cystine, cysteine-glutathione disulfide, carboxymethyl-cysteine, glutathione disulfide, carboxymethyl-glutathione. 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 Accela CTC","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":"350 μL/min","COLUMN_TEMPERATURE":"30","METHODS_FILENAME":"Metab_Orbitrap_Setup_v1_May_17_2013.docx","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","WEAK_WASH_SOLVENT_NAME":"H20 with 10% methanol","SAMPLE_SYRINGE_SIZE":"20μL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","SOFTWARE_VERSION":"Thermo Excalibur 2.2 SP1","ACQUISITION_DATE":"12/9/2013","ANALYSIS_PROTOCOL_FILE":"Metab_Quality_Control_v1_May_17_2013.docx, Metabolomics Core - Data Analysis.docx"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"technical triplicates for each sample","DATAFORMAT":".raw, .cdf","MS_RESULTS_FILE":"ST000592_AN000907_Results.txt"}

}