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Series GSE99486 Query DataSets for GSE99486
Status Public on Jun 01, 2017
Title Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study
Organisms Macaca mulatta; Plasmodium cynomolgi strain B
Experiment type Expression profiling by high throughput sequencing
Summary This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - 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 Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to three subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications of malaria. The anti-malarial drugs chloroquine and primaquine were administered to all remaining subjects at the end of the study for curative treatment of the liver- and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and at seven-time points from venous blood. The seven-time point collections were used to generate these results. This dataset was generated from whole blood samples from 5 individuals collected 7 times over the 100-day experiment. Since one animal was euthanized after time point 3 (meaning 4 potential samples were not collected from this animal, 2 samples failed library preparation, and one sample was collected from a blood transfusion donor animal, a total of 30 samples were collected. 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 04' (E04). To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics data sets, please visit http://plasmodb.org/plasmo/mahpic.jsp .
Web link http://www.systemsbiology.emory.edu/index.html http://plasmodb.org/plasmo/mahpic.jsp
 
Contributor(s) Arafat D, Bosinger S, Cabrera M, DeBarry JD, Galinski M, Garimalla S, Humphrey J, Karpuzoglu E, Kissinger JC, Lapp S, Lee K, Joice R, Joyner C, Meyer E, Moreno A, Nayak V, Nural M, Pakala S, Patel N, Tang Y, Tharp G
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA388645
Submission date May 31, 2017
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)
GPL25692 Illumina HiSeq 2000 (Macaca mulatta; Plasmodium cynomolgi strain B)
Samples (30)
GSM2644689 2080109_TimePoint1_WholeBlood
GSM2644690 2080111_TimePoint1_WholeBlood
GSM2644691 2080118_TimePoint1_WholeBlood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP108356

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

Supplementary file Size Download File type/resource
GSE99486_E04M99FGMmCyDaWB_Cynomolgi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 1.3 Mb (ftp)(http) XLSX
GSE99486_E04M99FGMmCyDaWB_IFX-11012018-RNA-Seq-Readme_MULTIPL_GEO.txt 27.0 Kb (ftp)(http) TXT
GSE99486_E04M99FGMmCyDaWB_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 4.6 Mb (ftp)(http) XLSX
GSE99486_E04M99FGMmCyDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 78.3 Kb (ftp)(http) PDF
GSE99486_E04M99FGMmDaCyWB_01232017-Analytical-Metadata_MULTIPL.xlsx 215.0 Kb (ftp)(http) XLSX
GSE99486_E04M99MEMmCyDaZZ_Supporting-Clinical-Information_XXXXXXX.pdf 230.8 Kb (ftp)(http) PDF
GSE99486_E04M99YSMmDaCyWB_Samples-1-30-IFX-Readme-11012018_MULTIPL_GEO.txt 13.9 Kb (ftp)(http) TXT
GSE99486_EN-RNeasy-Plus-Mini-Handbook_Qiagen_Sep2010_GEO.pdf 661.1 Kb (ftp)(http) PDF
GSE99486_Extraction_Whole_Blood_AppliedBiosystems_Part4329232RevD.pdf 376.0 Kb (ftp)(http) PDF
GSE99486_FxGen_RNAextractionWholeBlood_v1_Mar13_2013.pdf 463.5 Kb (ftp)(http) PDF
GSE99486_FxGen_read-mapping-normalization-and-data-analysis_v1.4_28August2014_GEO.pdf 214.0 Kb (ftp)(http) PDF
GSE99486_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE99486_RNA_Extraction_SOP_Mar_13_2013_GEO.pdf 228.0 Kb (ftp)(http) PDF
GSE99486_seq_template_v2.1_mahpic_E04FGWB.xls.gz 29.0 Kb (ftp)(http) XLS
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