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Series GSE58340 Query DataSets for GSE58340
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
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).
 
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.
Web link http://www.systemsbiology.emory.edu/index.html
 
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
Department Vaccine Center at Yerkes
Lab Galinski Lab
Street address 954 Gatewood Road
City Atlanta
State/province GA
ZIP/Postal code 30329
Country USA
 
Platforms (1)
GPL14954 Illumina HiSeq 2000 (Macaca mulatta)
Samples (70)
GSM1407424 2020519_TimePoint1_Blood
GSM1407425 2010301_TimePoint1_Blood
GSM1407426 2010212_TimePoint1_Blood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP043059

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Processed data is available on Series record
Raw data are available in SRA

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