NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE103259 Query DataSets for GSE103259
Status Public on Sep 01, 2017
Title Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from whole blood for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study
Organisms Macaca mulatta; Plasmodium coatneyi
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 four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 101 days, and pre- and post-101 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks.  The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 101 days. The different clinical phases of the infection were clinically determined for each subject.  Blood-stage curative doses of artemether were administered to all subjects at the end of the study.  Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. 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 101-day experiment. A total of 35 samples were collected. Within the MaHPIC, this project is known as ‘Experiment 03’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E03 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.  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/.
Web link http://plasmodb.org/plasmo/mahpic.jsp
 
Contributor(s) Bosinger SE, Cabrera-Mora M, Chien J, DeBarry JD, Galinski MR, Hoffman T, Humphrey JC, Jiang J, Joice-Cordy R, Joyner CJ, Kissinger JC, Lapp SA, Lackman N, Meyer EV, Moreno A, Nural M, Pakala SB, Patel N, Stealey HM, Tharp G
Citation(s) 31045574
BioProject PRJNA400695
Submission date Aug 29, 2017
Last update date Jun 21, 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)
GPL25689 Illumina HiSeq 1000 (Macaca mulatta; Plasmodium coatneyi)
Samples (35)
GSM2759329 2227479_TimePoint1_WholeBlood
GSM2759330 2231906_TimePoint1_WholeBlood
GSM2759331 2231907_TimePoint1_WholeBlood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP116593

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
GSE103259_E03M99FGMmCoDaWB_11012018-Readme_MULTIPL_GEO.txt 24.0 Kb (ftp)(http) TXT
GSE103259_E03M99FGMmCoDaWB_Analytical-Metadata_MULTIPL.xlsx 56.4 Kb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaWB_Coatneyi-Genes-DESeq2NormalizedCounts-Results_MULTIPL.xlsx 682.1 Kb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaWB_Coatneyi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 953.3 Kb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaWB_ERCC-Controls-RawCounts-Results_MULTIPL.xlsx 47.6 Kb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaWB_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL_GEO.xlsx 7.6 Mb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL.xlsx 3.6 Mb (ftp)(http) XLSX
GSE103259_E03M99FGMmCoDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 79.7 Kb (ftp)(http) PDF
GSE103259_E03M99MEMmCoDaZZ_Supporting-Clinical-Information_MULTIPL.pdf 257.3 Kb (ftp)(http) PDF
GSE103259_E03M99YSMmCoDaWB_11012018-Readme_MULTIPL_GEO.txt 19.4 Kb (ftp)(http) TXT
GSE103259_E03M99YSMmCoDaWB_Analytical-Metadata-01152016_MULTIPL.xlsx 237.7 Kb (ftp)(http) XLSX
GSE103259_E03_Coatneyi-Clinical-Classification.xlsx 26.1 Kb (ftp)(http) XLSX
GSE103259_EN-RNeasy-Plus-Mini-Handbook_Qiagen_Sep2010.pdf 661.1 Kb (ftp)(http) PDF
GSE103259_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE103259_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE103259_FxGen_read-mapping-and-data-processing_V2.1.pdf 58.8 Kb (ftp)(http) PDF
GSE103259_MaHPIC_File_Naming_Standards_2_23_2018.pdf 211.5 Kb (ftp)(http) PDF
GSE103259_Tempus_Spin_RNA_Isolation_Kit_Rev_D_112008.pdf 375.9 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap