#METABOLOMICS WORKBENCH mahpic_infodepo_20170405_132556 DATATRACK_ID:879 STUDY_ID:ST000592 ANALYSIS_ID:AN000907 PROJECT_ID:PR000384 VERSION 1 CREATED_ON April 17, 2017, 10:07 am #PROJECT PR:PROJECT_TITLE The Malaria Host-Pathogen Interaction Center (MaHPIC) PR:PROJECT_TYPE Systems Biology PR:PROJECT_SUMMARY The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary PR:PROJECT_SUMMARY malaria systems biology research program supported by an NIH/NIAID contract (# PR:PROJECT_SUMMARY HHSN272201200031C; see http://www.systemsbiology.emory.edu). The MaHPIC PR:PROJECT_SUMMARY generates many data types (e.g., clinical, parasitological, metabolomics, PR:PROJECT_SUMMARY functional genomics, lipidomics, proteomics, immune response) and mathematical PR:PROJECT_SUMMARY models, to iteratively test and develop hypotheses related to the complex PR:PROJECT_SUMMARY host-parasite dynamics in the course of malaria in non-human primates, and PR:PROJECT_SUMMARY metabolomics data via collaborations with investigators conducting clinical PR:PROJECT_SUMMARY studies in malaria endemic countries, with the overarching goal of better PR:PROJECT_SUMMARY understanding human disease, pathogenesis, and immunity. Curation and PR:PROJECT_SUMMARY maintenance of all data and metadata are the responsibility of the MaHPIC. PR:INSTITUTE Emory University PR:DEPARTMENT School of Medicine, Vaccine Center at Yerkes PR:LAST_NAME Galinski PR:FIRST_NAME Mary PR:ADDRESS Emory University, 954 Gatewood Rd, Room 208, Atlanta, GA 30329 PR:EMAIL mahpic@emory.edu PR:PHONE none PR:FUNDING_SOURCE NIAID Contract: # HHSN272201200031C #STUDY ST:STUDY_TITLE Experiment 13: Uninfected Macaca mulatta exposed to pyrimethamine to produce and ST:STUDY_TITLE integrate clinical, hematological, and omics control measures. ST:STUDY_SUMMARY Uninfected, malaria-naive, male rhesus macaques (Macaca mulatta), approximately ST:STUDY_SUMMARY two years of age, were inoculated intravenously with a preparation of salivary ST:STUDY_SUMMARY gland material derived from non-infected Anopheles dirus and profiled for ST:STUDY_SUMMARY clinical, hematological, functional genomic, lipidomic, proteomic, and ST:STUDY_SUMMARY metabolomic measurements. Samples were generated and analyzed to investigate the ST:STUDY_SUMMARY effects of the pharmacological intervention with the anti-malarial drug ST:STUDY_SUMMARY pyrimethamine on normal individuals. The experiment was designed for 100 days ST:STUDY_SUMMARY plus a follow-up period, with pyrimethamine administered at three different time ST:STUDY_SUMMARY points to coincide with the predicted treatment days of experimentally infected ST:STUDY_SUMMARY rhesus macaques. Capillary blood samples were collected daily for the ST:STUDY_SUMMARY measurement of CBCs and reticulocytes. Capillary blood samples were collected ST:STUDY_SUMMARY every other day to obtain plasma for metabolomic analysis. Venous blood samples ST:STUDY_SUMMARY and bone marrow aspirates were collected at seven time points before and after ST:STUDY_SUMMARY three rounds of drug administration for functional genomic, proteomic, and ST:STUDY_SUMMARY lipidomic analyses. Within the MaHPIC, this project is known as 'Experiment 13'. ST:STUDY_SUMMARY This dataset was produced by Dean Jones at Emory University. The following ST:STUDY_SUMMARY contributed to the creation of this dataset: The MaHPIC Consortium, John ST:STUDY_SUMMARY Barnwell, Monica Cabrera, Jeremy D. DeBarry, Mary Galinski, Trenton Hoffman, Jay ST:STUDY_SUMMARY Humphrey, Jianlin Jiang, Chet Joyner, Nicolas Lackman, Stacey Lapp, Esmeralda ST:STUDY_SUMMARY Meyer, Alberto Moreno, Mustafa Nural, and Suman Pakala. The experimental design ST:STUDY_SUMMARY and protocols for this study were approved by the Emory University Institutional ST:STUDY_SUMMARY Animal Care and Use Committee (IACUC). ST:INSTITUTE Emory University ST:DEPARTMENT School of Medicine, Vaccine Center at Yerkes ST:LAST_NAME Galinksi ST:FIRST_NAME Mary ST:ADDRESS Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room ST:ADDRESS 003, Atlanta, GA 30329 ST:EMAIL mahpic@emory.edu ST:PHONE none ST:TOTAL_SUBJECTS 6 ST:STUDY_COMMENTS 31 samples, "The experimental design and protocols for this study were ST:STUDY_COMMENTS approved by the Emory University Institutional Animal Care and Use Committee ST:STUDY_COMMENTS (IACUC). These results are a product of a consortium of researchers known as the ST:STUDY_COMMENTS Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the ST:STUDY_COMMENTS MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, ST:STUDY_COMMENTS these data were collected as part of 'Experiment 13' (E13). To access other ST:STUDY_COMMENTS publicly available results from E13 and other MaHPIC Experiments, including ST:STUDY_COMMENTS clinical results (specifics on drugs administered, diet, and veterinary ST:STUDY_COMMENTS interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . ST:STUDY_COMMENTS This page will be updated as datasets are released to the public. See Pubmed ST:STUDY_COMMENTS ID:25453034 for the associated publication for this study." #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Macaca mulatta SU:TAXONOMY_ID 9544 SU:GENOTYPE_STRAIN N/A|6.53kg|6.87kg|6.09kg|7.23kg|6.48kg SU:GENDER Male| Male| Male| Male| Male| Male SU:ANIMAL_ANIMAL_SUPPLIER none|Yerkes Field Station|Yerkes Primate Research Center|Yerkes Primate Research SU:ANIMAL_ANIMAL_SUPPLIER Center| |Yerkes Primate Research Center SU:ANIMAL_HOUSING Metallic|Metallic|Metallic|Metallic|Metallic|Metallic SU:ANIMAL_LIGHT_CYCLE 12/11|12/12|12/12|12/12|12/12|12/12 SU:ANIMAL_FEED Monkey Jumbo Diet 5037 and 5038 SU:ANIMAL_WATER tap in bottle SU:ANIMAL_INCLUSION_CRITERIA Weight #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS RCs13 1906030 Collection Type:Time Point 3 Gender=Male SUBJECT_SAMPLE_FACTORS RCs13 1932199 Collection Type:Time Point 4 Gender=Male SUBJECT_SAMPLE_FACTORS RCs13 1941204 Collection Type:Time Point 5 Gender=Male SUBJECT_SAMPLE_FACTORS RCs13 1968402 Collection Type:Time Point 6 Gender=Male SUBJECT_SAMPLE_FACTORS RCs13 1972662 Collection Type:Time Point 7 Gender=Male SUBJECT_SAMPLE_FACTORS REe6 1892525 Collection Type:Reference Gender=Male SUBJECT_SAMPLE_FACTORS RTi13 1906044 Collection Type:Time Point 3 Gender=Male SUBJECT_SAMPLE_FACTORS RTi13 1932200 Collection Type:Time Point 4 Gender=Male SUBJECT_SAMPLE_FACTORS RTi13 1941205 Collection Type:Time Point 5 Gender=Male SUBJECT_SAMPLE_FACTORS RTi13 1968432 Collection Type:Time Point 6 Gender=Male SUBJECT_SAMPLE_FACTORS RTi13 1972668 Collection Type:Time Point 7 Gender=Male SUBJECT_SAMPLE_FACTORS RUn13 1906045 Collection Type:Time Point 3 Gender=Male SUBJECT_SAMPLE_FACTORS RUn13 1932201 Collection Type:Time Point 4 Gender=Male SUBJECT_SAMPLE_FACTORS RUn13 1941206 Collection Type:Time Point 5 Gender=Male SUBJECT_SAMPLE_FACTORS RUn13 1968433 Collection Type:Time Point 6 Gender=Male SUBJECT_SAMPLE_FACTORS RUn13 1972674 Collection Type:Time Point 7 Gender=Male SUBJECT_SAMPLE_FACTORS RWr13 1906046 Collection Type:Time Point 3 Gender=Male SUBJECT_SAMPLE_FACTORS RWr13 1932202 Collection Type:Time Point 4 Gender=Male SUBJECT_SAMPLE_FACTORS RWr13 1941207 Collection Type:Time Point 5 Gender=Male SUBJECT_SAMPLE_FACTORS RWr13 1968434 Collection Type:Time Point 6 Gender=Male SUBJECT_SAMPLE_FACTORS RWr13 1972680 Collection Type:Time Point 7 Gender=Male SUBJECT_SAMPLE_FACTORS RZe13 1906047 Collection Type:Time Point 3 Gender=Male SUBJECT_SAMPLE_FACTORS RZe13 1932203 Collection Type:Time Point 4 Gender=Male SUBJECT_SAMPLE_FACTORS RZe13 1941208 Collection Type:Time Point 5 Gender=Male SUBJECT_SAMPLE_FACTORS RZe13 1968435 Collection Type:Time Point 6 Gender=Male SUBJECT_SAMPLE_FACTORS RZe13 1972686 Collection Type:Time Point 7 Gender=Male SUBJECT_SAMPLE_FACTORS N/A 9991200135 Collection Type:QC Sample, in-lab prepared Gender=Male SUBJECT_SAMPLE_FACTORS N/A 9991200136 Collection Type:QC Sample, in-lab prepared Gender=Male SUBJECT_SAMPLE_FACTORS N/A 9991100046 Collection Type:QC Sample, from NIST Gender=Male SUBJECT_SAMPLE_FACTORS N/A 9991200137 Collection Type:QC Sample, in-lab prepared Gender=Male SUBJECT_SAMPLE_FACTORS N/A 9991100047 Collection Type:QC Sample, from NIST Gender=Male #COLLECTION CO:COLLECTION_SUMMARY Time Point 3 Post-Rx: "Observations on NHP response six days after CO:COLLECTION_SUMMARY administration of Pyrimethamine"|Time Point 4 Rx: "Pyrimethamine was CO:COLLECTION_SUMMARY administered at 1 mg/kg/day IM for three days"|Time Point 5 Post-Rx: CO:COLLECTION_SUMMARY "Observations on NHP response seven days after initiation of the anti-malarial CO:COLLECTION_SUMMARY regimen"|Time Point 6 Rx: "Pyrimethamine was administered at 1 mg/kg/day IM for CO:COLLECTION_SUMMARY three days"|Time Point 7 Post-Rx: "Observations on NHP response eight days after CO:COLLECTION_SUMMARY initiation of the anti-malarial regimen" CO:SAMPLE_TYPE Whole blood CO:COLLECTION_METHOD Intravenous CO:COLLECTION_FREQUENCY once CO:BLOOD_SERUM_OR_PLASMA Plasma #TREATMENT TR:TREATMENT_SUMMARY None #SAMPLEPREP SP:SAMPLEPREP_SUMMARY aliquots of 65ul sample were mixed with 130ul acetonitrile and 3.25ul internal SP:SAMPLEPREP_SUMMARY standard. Keep on ice for 30 minutes and vortex every 15 minutes. Centrifuge for SP:SAMPLEPREP_SUMMARY 10 minutes at 13.2rpm and 4C. Using a pipette, 130ul of supernatant was removed SP:SAMPLEPREP_SUMMARY and placed into autosampler vials for the mass spectrometer. SP:SAMPLEPREP_PROTOCOL_FILENAME Metab_Sample_Preparation_Plasma_serum_v1_May_17_2013.docx SP:PROCESSING_METHOD Precipitation of protein, centrifuge, and remove supernatant SP:PROCESSING_STORAGE_CONDITIONS On ice SP:EXTRACTION_METHOD 1:2 sample:acetonitrile SP:EXTRACT_STORAGE Pipette supernatant into autosampler vials for mass spectrometer SP:SAMPLE_SPIKING C18 standards: Caffeine and Diethyl-toluamide. Anion Exchange Standards: SP:SAMPLE_SPIKING Cystine, cysteine-glutathione disulfide, carboxymethyl-cysteine, glutathione SP:SAMPLE_SPIKING disulfide, carboxymethyl-glutathione. Stable isotopes: [13C6]-D-glucose, SP:SAMPLE_SPIKING [15N]-indole, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, SP:SAMPLE_SPIKING [2-15N]-L-lysine dihydrochloride, [15N]-choline chloride, [13C5]-L-glutamic SP:SAMPLE_SPIKING acid, [13C7]-benzoic acid, [15N]-L-tyrosine, [15N2]-uracil, SP:SAMPLE_SPIKING [3,4-13C2]-cholesterol, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, SP:SAMPLE_SPIKING U-15N2]-L-glutamine. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY untargeted chromatography (C18 column) CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Accela CTC CH:COLUMN_NAME Higgins C18 100x2.1mm, 5um CH:FLOW_GRADIENT A%: 0-10mins = 5%; B%: 0-2mins = 35%, 2-7mins = gradient to 95%, 7-10mins = 95%; CH:FLOW_GRADIENT C%: 0-2mins = 60%, 2-7mins = gradient to 0%, 7-10mins = 0% CH:FLOW_RATE 350 μL/min CH:COLUMN_TEMPERATURE 30 CH:METHODS_FILENAME Metab_Orbitrap_Setup_v1_May_17_2013.docx CH:SOLVENT_A LC grade H2O with 2% Formic Acid CH:SOLVENT_B Acetonitrile (LC grade) CH:COLUMN_PRESSURE 200 Bar (max) CH:INJECTION_TEMPERATURE 4C CH:INTERNAL_STANDARD Caffeine, Diethyl-toluamide CH:INTERNAL_STANDARD_MT 1.5 min; 6-6.6 min CH:SAMPLE_INJECTION 10μL CH:SAMPLING_CONE ESI: HESI probe with S-lens combination CH:ANALYTICAL_TIME 10 minutes CH:CAPILLARY_VOLTAGE 4.6 kV CH:OVEN_TEMPERATURE 45C CH:RUNNING_VOLTAGE 4.6 kV CH:WEAK_WASH_SOLVENT_NAME H20 with 10% methanol CH:SAMPLE_SYRINGE_SIZE 20μL #ANALYSIS AN:ANALYSIS_TYPE MS AN:SOFTWARE_VERSION Thermo Excalibur 2.2 SP1 AN:ACQUISITION_DATE 12/9/2013 AN:ANALYSIS_PROTOCOL_FILE Metab_Quality_Control_v1_May_17_2013.docx, Metabolomics Core - Data AN:ANALYSIS_PROTOCOL_FILE Analysis.docx #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS technical triplicates for each sample MS:DATAFORMAT .raw, .cdf MS:MS_RESULTS_FILE ST000592_AN000907_Results.txt #END