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Series GSE103042 Query DataSets for GSE103042
Status Public on Aug 24, 2017
Title Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from bone marrow 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 [Original Title] Malaria Host Pathogen Interaction Center Experiment 03: Host and parasite gene transcript abundance measures from bone marrow for Macaca mulatta infected with Plasmodium coatneyi Hackeri strain from 7 time points over a 101 day study of acute, recrudescent, and chronic infections.
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 bone marrow 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 Drs. Mark P. Styczynski and Yan Tang at Georgia Institute of Technology and 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://www.systemsbiology.emory.edu/index.htmlhttp://plasmodb.org/plasmo/mahpic.jsp
 
Contributor(s) Bosinger SE, Cabrera-Mora M, Chien J, DeBarry JD, Galinski MR, Hoffman T, Humphrey JC, Jiang J, Cordy RJ, Joyner CJ, Kissinger JC, Lapp SA, Lackman N, Meyer EV, Moreno A, Nural M, Pakala SB, Patel N, Styczynski MP, Tang Y, Tharp G
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA400137
Submission date Aug 24, 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)
GPL25689 Illumina HiSeq 1000 (Macaca mulatta; Plasmodium coatneyi)
Samples (35)
GSM2753139 2319002_TimePoint3_BoneMarrow
GSM2753140 2319003_TimePoint6_BoneMarrow
GSM2753141 2319004_TimePoint4_BoneMarrow
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP116117

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Supplementary file Size Download File type/resource
GSE103042_E03M99FGMmCoDaBM_11012018-Readme_MULTIPL_GEO.txt 19.5 Kb (ftp)(http) TXT
GSE103042_E03M99FGMmCoDaBM_Analytical-Metadata_MULTIPL.xlsx 16.2 Kb (ftp)(http) XLSX
GSE103042_E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 917.7 Kb (ftp)(http) XLSX
GSE103042_E03M99FGMmCoDaBM_Coatneyi-Genes-RawCounts-Results_MULTIPL.xlsx 705.6 Kb (ftp)(http) XLSX
GSE103042_E03M99FGMmCoDaBM_FxGen_read-mapping-normalization-and-data-analysis.pdf 260.5 Kb (ftp)(http) PDF
GSE103042_E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 7.6 Mb (ftp)(http) XLSX
GSE103042_E03M99FGMmCoDaBM_Mulatta-Genes-RawCounts-Results_MULTIPL.xlsx 3.6 Mb (ftp)(http) XLSX
GSE103042_E03M99FGMmCoDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 79.7 Kb (ftp)(http) PDF
GSE103042_E03M99MEMmCoDaZZ_Supporting-Clinical-Information_MULTIPL.pdf 257.3 Kb (ftp)(http) PDF
GSE103042_E03M99YSMmCoDaBM_11012018-Readme_MULTIPL_GEO.txt 19.4 Kb (ftp)(http) TXT
GSE103042_E03M99YSMmCoDaBM_IFX-Analytical-Metadata_MULTIPL.xlsx 238.1 Kb (ftp)(http) XLSX
GSE103042_EN-RNeasy-Plus-Mini-Handbook_Qiagen_Sep2010.pdf 661.1 Kb (ftp)(http) PDF
GSE103042_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE103042_Tempus_Spin_RNA_Isolation_Kit_Rev_D_112008.pdf 375.9 Kb (ftp)(http) PDF
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