Summary of Study ST000592

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000384. The data can be accessed directly via it's Project DOI: 10.21228/M8DP41 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000592
Study TitleUninfected Macaca mulatta exposed to pyrimethamine to produce and integrate clinical, hematological, and omics control measures.
Study SummaryUninfected, 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
DepartmentSchool of Medicine, Vaccine Center at Yerkes
Last NameGalinksi
First NameMary
AddressEmory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
Emailmahpic@emory.edu
Phonenone
Submit Date2017-04-05
Total Subjects6
Study Comments31 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. " Publication: (PMC4233942) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233942/
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-07-10
Release Version1
Mary Galinksi Mary Galinksi
https://dx.doi.org/10.21228/M8DP41
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000384
Project DOI:doi: 10.21228/M8DP41
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, Atlanta, GA 30329
Email:mgalins@emory.edu
Phone:N/A
Funding Source:NIAID Contract: # HHSN272201200031C

Subject:

Subject ID:SU000615
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
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Macaca mulatta (Factor headings shown in green)

mb_sample_id local_sample_id Collection Type
SA0326059991100047QC Sample, from NIST
SA0326069991100046QC Sample, from NIST
SA0326079991200136QC Sample, in-lab prepared
SA0326089991200137QC Sample, in-lab prepared
SA0326099991200135QC Sample, in-lab prepared
SA0326101892525Reference
SA0326111906047Time Point 3
SA0326121906030Time Point 3
SA0326131906046Time Point 3
SA0326141906044Time Point 3
SA0326151906045Time Point 3
SA0326161932200Time Point 4
SA0326171932202Time Point 4
SA0326181932203Time Point 4
SA0326191932199Time Point 4
SA0326201932201Time Point 4
SA0326211941208Time Point 5
SA0326221941206Time Point 5
SA0326231941205Time Point 5
SA0326241941204Time Point 5
SA0326251941207Time Point 5
SA0326261968402Time Point 6
SA0326271968435Time Point 6
SA0326281968432Time Point 6
SA0326291968433Time Point 6
SA0326301968434Time Point 6
SA0326311972674Time Point 7
SA0326321972662Time Point 7
SA0326331972668Time Point 7
SA0326341972680Time Point 7
SA0326351972686Time Point 7
Showing results 1 to 31 of 31

Collection:

Collection ID:CO000609
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 ID:TR000629
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000622
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.

Combined analysis:

Analysis ID AN000907 AN000908
Analysis type MS MS
Chromatography type Reversed phase Ion exchange
Chromatography system Thermo Accela CTC Thermo Accela CTC
Column Higgins C18 (100 x 2.1mm,5um) Hamilton Anion Exchange (100 x 2.1mm,7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE
Units unspecified unspecified

Chromatography:

Chromatography ID:CH000644
Chromatography Summary:untargeted chromatography (C18 column)
Methods Filename:Metab_Orbitrap_Setup_v1_May_17_2013.docx
Instrument Name:Thermo Accela CTC
Column Name:Higgins C18 (100 x 2.1mm,5um)
Column Pressure:200 Bar (max)
Column Temperature:30
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
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
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile
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
Chromatography Type:Reversed phase
  
Chromatography ID:CH000645
Chromatography Summary:anion exchange chromatography
Methods Filename:Metab_Orbitrap_Setup_v1_May_17_2013.docx
Instrument Name:Thermo Accela CTC
Column Name:Hamilton Anion Exchange (100 x 2.1mm,7um)
Column Pressure:200 Bar (max)
Column Temperature:30
Flow Gradient:A%: 0-2mins = 5%, 2-7mins = gradient to 50%, 7-10mins = 50%; B%: 0-10mins = 50%; C%: 0-2mins = 45%, 2-7mins = gradient to 0%, 7-10mins = 0%
Flow Rate:350 μL/min
Injection Temperature:4C
Internal Standard:Cystine; cysteine-glutathione disulfide; carboxymethyl-cysteine (very low); glutathione disulfide (+1 and +2); carboxymethyl-glutathione
Internal Standard Mt:1-1.5 min; 2-4 min; 3.5-5 min; 7-8 min; 7-8 min
Sample Injection:10μL
Sampling Cone:ESI: HESI probe with S-lens combination
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile
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
Chromatography Type:Ion exchange

MS:

MS ID:MS000806
Analysis ID:AN000907
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:technical triplicates for each sample
Ion Mode:POSITIVE
Dataformat:.raw, .cdf
Analysis Protocol File:Metab_Quality_Control_v1_May_17_2013.docx
Metabolomics Core - Data
Analysis.docx
  
MS ID:MS000807
Analysis ID:AN000908
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:technical triplicates for each sample
Ion Mode:POSITIVE
Dataformat:.raw, .cdf
Analysis Protocol File:Metab_Quality_Control_v1_May_17_2013.docx
Metabolomics Core - Data
Analysis.docx
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