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Series GSE94273 Query DataSets for GSE94273
Status Public on Apr 12, 2017
Title Malaria Host Pathogen Interaction Center Experiment 04: Host and parasite gene transcript abundances, from bone marrow aspirate, 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 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 (MaHPIC Program Director), Jessica Kissinger (MaHPIC Co-Program Director), and Alberto Moreno (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 bone marrow aspirate samples from 5 individuals collected 7 times over the 100-day experiment. Since one animal was euthanized after time point 3, a total of 31 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 . 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 .
Web link
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(s) 28938907
BioProject PRJNA385819
Submission date Jan 30, 2017
Last update date Sep 13, 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 (31)
GSM2472050 2131269_TimePoint1_BoneMarrow
GSM2472051 2131272_TimePoint1_BoneMarrow
GSM2472052 2131275_TimePoint1_BoneMarrow
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
SRA SRP106638

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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
GSE94273_E04M99FGMmCyDaBM_Cynomolgi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 1.2 Mb (ftp)(http) XLSX
GSE94273_E04M99FGMmCyDaBM_IFX-11012018-RNA-Seq-Readme_MULTIPL_GEO.txt 26.6 Kb (ftp)(http) TXT
GSE94273_E04M99FGMmCyDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx 4.9 Mb (ftp)(http) XLSX
GSE94273_E04M99FGMmCyDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 78.3 Kb (ftp)(http) PDF
GSE94273_E04M99FGMmDaCyBM_01232017-Analytical-Metadata_MULTIPL.xlsx 223.8 Kb (ftp)(http) XLSX
GSE94273_E04M99MEMmCyDaZZ_Supporting-Clinical-Information_XXXXXXX.pdf 230.8 Kb (ftp)(http) PDF
GSE94273_E04M99YSMmDaCyBM_Samples-31-61-IFX-Readme-11012018_MULTIPL_GEO.txt 14.4 Kb (ftp)(http) TXT
GSE94273_EN-RNeasy-Plus-Mini-Handbook_Qiagen_Sep2010_GEO.pdf 661.1 Kb (ftp)(http) PDF
GSE94273_FxGen_RNAextractionBoneMarrow_v1_Mar13_2013_GEO.pdf 216.4 Kb (ftp)(http) PDF
GSE94273_FxGen_read-mapping-normalization-and-data-analysis_v1.4_28August2014_GEO.pdf 214.0 Kb (ftp)(http) PDF
GSE94273_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE94273_RNA_Extraction_SOP_Mar_13_2013_GEO.pdf 228.0 Kb (ftp)(http) PDF
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