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| Status |
Public on Oct 10, 2014 |
| Title |
Malaria Host Pathogen Interaction Center Experiment 13: Gene and exon transcript abundances of uninfected Macaca mulatta treated with pyrimethamine over 7 time points in a 100 day study |
| Organism |
Macaca mulatta |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) 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 (NHPs), 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), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).
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| Overall design |
The experimental design of this pyrimethamine administration experiment with Macaca mulatta was approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and is as follows. Five naive males (RCs13, RWr13, RUn13, RZe13 and RTi13) approximately 2 years of age were injected intravenously with a preparation of Anopheles dirus salivary gland material and then profiled for clinical and omic measurements over the course of a 100-day experiment. Samples were generated and analyzed as part of a multi-omic approach to understanding the effects that the anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (M. mulatta). There was no infection with Plasmodium parasites during this study. Whole blood and bone marrow RNA-Seq and plasma have been obtained for seven time-points before, during and after three rounds of drug administration. Samples are from either whole blood or bone marrow specimen types. 5 individuals were sampled for each specimen type, 7 times each over the 100 day experiment. 5 individuals * 2 specimen types * 7 time points = 70 samples.
Biological samples (Whole Blood or Bone Marrow) were collected at 7 time points during the 100 days. These correspond to:
Time Point 1 = Day 0 (Baseline Sampling Point) Time Point 2 = Day 21 Time Point 3 = Day 27 Time Point 4 = Day 52 Time Point 5 = Day 59 Time Point 6 = Day 90 Time Point 7 = Day 98
Pyrimethamine was administered on Days 21, 52, 53, 54, 90, 91, and 92.
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| Web link |
http://www.systemsbiology.emory.edu/index.html
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| Contributor(s) |
Gibson G, Galinski MR, Moreno A, Kissinger JC, Styczynski M, Lee K, Pakala SP, Nayak V, Lapp S, Tran V, Uppal K, Jones D, Arafat D, Meyer E, Cabrera M, Tang Y, Yin W, DeBarry JD |
| Citation(s) |
25453034 |
| BioProject |
PRJNA385821 |
| Submission date |
Jun 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Galinski |
| Organization name |
Emory University
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| Department |
Vaccine Center at Yerkes
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| Lab |
Galinski Lab
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| Street address |
954 Gatewood Road
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
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| Platforms (1) |
| GPL14954 |
Illumina HiSeq 2000 (Macaca mulatta) |
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| Samples (70)
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| This SubSeries is part of SuperSeries: |
| GSE94274 |
An Integrated Approach to Understanding Host-Pathogen Interactions |
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| Relations |
| SRA |
SRP043059 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58340_E13M99FGMmDpXXXX_Samples-1-24-Analytical-Metadata_MULTIPL.xlsx |
213.3 Kb |
(ftp)(http) |
XLSX |
| GSE58340_E13M99FGMmDpXXXX_Samples-25-48-Analytical-Metadata_MULTIPL.xlsx |
213.7 Kb |
(ftp)(http) |
XLSX |
| GSE58340_E13M99FGMmDpXXXX_Samples-49-72-Analytical-Metadata_MULTIPL.xlsx |
155.5 Kb |
(ftp)(http) |
XLSX |
| GSE58340_E13M99FGMmDpXXZZ_11022018-Readme_MULTIPL_GEO.txt |
13.1 Kb |
(ftp)(http) |
TXT |
| GSE58340_E13M99FGMmDpXXZZ_DESeq-SOPv1-1-exonLibSizeNormalized_MULTIPL_GEO.xlsx.gz |
131.5 Mb |
(ftp)(http) |
XLSX |
| GSE58340_E13M99FGMmDpXXZZ_DESeq-SOPv1-1-genelibSizeNormalized_MULTIPL_GEO.xlsx.gz |
13.3 Mb |
(ftp)(http) |
XLSX |
| GSE58340_E13M99MEMmXXDpWB_Experiment-Summary-Diagram-Supplementary_MULTIPL.pdf |
67.4 Kb |
(ftp)(http) |
PDF |
| GSE58340_MaHPIC_File_Naming_Standards_2_23_2018.pdf |
96.4 Kb |
(ftp)(http) |
PDF |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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