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.
| Study ID | ST000592 |
| Study Title | 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 |
| mahpic@emory.edu | |
| Phone | none |
| Submit Date | 2017-04-05 |
| 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. " Publication: (PMC4233942) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233942/ |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-07-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Animal; Subject species: Macaca mulatta (Factor headings shown in green)
| mb_sample_id | local_sample_id | Collection Type |
|---|---|---|
| SA032605 | 9991100047 | QC Sample, from NIST |
| SA032606 | 9991100046 | QC Sample, from NIST |
| SA032607 | 9991200136 | QC Sample, in-lab prepared |
| SA032608 | 9991200137 | QC Sample, in-lab prepared |
| SA032609 | 9991200135 | QC Sample, in-lab prepared |
| SA032610 | 1892525 | Reference |
| SA032611 | 1906047 | Time Point 3 |
| SA032612 | 1906030 | Time Point 3 |
| SA032613 | 1906046 | Time Point 3 |
| SA032614 | 1906044 | Time Point 3 |
| SA032615 | 1906045 | Time Point 3 |
| SA032616 | 1932200 | Time Point 4 |
| SA032617 | 1932202 | Time Point 4 |
| SA032618 | 1932203 | Time Point 4 |
| SA032619 | 1932199 | Time Point 4 |
| SA032620 | 1932201 | Time Point 4 |
| SA032621 | 1941208 | Time Point 5 |
| SA032622 | 1941206 | Time Point 5 |
| SA032623 | 1941205 | Time Point 5 |
| SA032624 | 1941204 | Time Point 5 |
| SA032625 | 1941207 | Time Point 5 |
| SA032626 | 1968402 | Time Point 6 |
| SA032627 | 1968435 | Time Point 6 |
| SA032628 | 1968432 | Time Point 6 |
| SA032629 | 1968433 | Time Point 6 |
| SA032630 | 1968434 | Time Point 6 |
| SA032631 | 1972674 | Time Point 7 |
| SA032632 | 1972662 | Time Point 7 |
| SA032633 | 1972668 | Time Point 7 |
| SA032634 | 1972680 | Time Point 7 |
| SA032635 | 1972686 | Time 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 |
