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Series GSE104223 Query DataSets for GSE104223
Status Public on Sep 27, 2017
Title Malaria Host Pathogen Interaction Center Experiment 23R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain 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 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 about 100 days, with pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. During the 100-day period subjects experienced periods of patent and sub-patent infection. The anti-malarial drug artemether was subcuratively administered to subjects after the initial peak of infection, if subjects were not able to self-resolve. Blood-stage curative artemether was administered to all subjects following peak infection, and following a period of relapse infection. All peaks were clinically determined for each subject. The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. 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. E23 is an iteration of Experiment 04 with the same parasite-host combination. E23 is the first in a series of experiments that includes subsequent homologous (Experiment 24, P. cynomolgi B strain) and heterologous (Experiment 25, P. cynomolgi strain ceylonensis) challenges of individuals from the E23 cohort. Note that one E23 subject was not included in subsequent experiments due to persistent behavioral issues that prevented sample collection. Within the MaHPIC, this project is known as ‘Experiment 23R’. E23R is a 'resequencing' of all samples from E23, processed with SOPs and technology consistent with that used for E04R, E24, and E25 so that results from these experiments could be reliably compared. Only E23R is intended for comparison with E04R, E24, and E25. 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 E23R 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).
Web link http://www.systemsbiology.emory.edu/index.htmlhttp://plasmodb.org/plasmo/mahpic.jsp
 
Contributor(s) Barnwell JW, Bosinger SE, Cabrera-Mora M, Cordy RJ, DeBarry JD, Galinski MR, Hankus A, Humphrey JC, Jiang J, Joyner CJ, Lackman N, Lapp SA, Moreno A, Nural M, Pakala SB, Patel N, Stealey HM, Tharp G
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA412080
Submission date Sep 25, 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)
GPL25691 Illumina HiSeq 3000 (Macaca mulatta; Plasmodium cynomolgi strain B)
Samples (48)
GSM2792848 2621351_TimePoint1A_WholeBlood
GSM2792849 2621352_TimePoint1_WholeBlood
GSM2792850 2621353_TimePoint1B_WholeBlood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP118827

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
GSE104223_E23M99MEMmCyDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 63.1 Kb (ftp)(http) PDF
GSE104223_E23M99MEMmCyDaZZ_Supporting-Clinical-Information_MULTIPL.pdf 252.4 Kb (ftp)(http) PDF
GSE104223_E23RM99FGMmCyDaWB_11022018-Readme_MULTIPL_GEO.txt 22.2 Kb (ftp)(http) TXT
GSE104223_E23RM99FGMmCyDaWB_Analytical-Metadata_MULTIPL.xlsx 58.2 Kb (ftp)(http) XLSX
GSE104223_E23RM99FGMmCyDaWB_Cynomolgi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 1.4 Mb (ftp)(http) XLSX
GSE104223_E23RM99FGMmCyDaWB_ERCC-Controls-RawCounts-Results_MULTIPL.xlsx 49.5 Kb (ftp)(http) XLSX
GSE104223_E23RM99FGMmCyDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 4.8 Mb (ftp)(http) XLSX
GSE104223_E23RM99YSMmCyDaWB_11022018-README_MULTIPL_GEO.txt 22.9 Kb (ftp)(http) TXT
GSE104223_E23RM99YSMmCyDaWB_Analytical-Metadata_MULTIPL.xlsx 36.7 Kb (ftp)(http) XLSX
GSE104223_E23RT1BYSMmCyDaWB_Run2-Analytical-Metadata_2621369.xlsx 91.0 Kb (ftp)(http) XLSX
GSE104223_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE104223_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE104223_FxGen_read-mapping-and-data-processing_V2.0.pdf 36.3 Kb (ftp)(http) PDF
GSE104223_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE104223_YS_SOP_E23R_ClontechV4_SingleCell_cDNASynthesis.pdf 123.5 Kb (ftp)(http) PDF
GSE104223_YS_SOP_E23R_Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE104223_nextera-xt-library-prep-protocol-guide-1000000006564-00.pdf 282.8 Kb (ftp)(http) PDF
GSE104223_seq_template_v2.1_mahpic_E23RFGWB_GEO.xlsx 114.0 Kb (ftp)(http) XLSX
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