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Series GSE104101 Query DataSets for GSE104101
Status Public on Sep 26, 2017
Title Malaria Host Pathogen Interaction Center Experiment 24: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi B strain treated with artemether over 3 time points in a 46 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 Male rhesus macaques (Macaca mulatta), cleared of previous infection with P. cynomolgi B strain via treatment with the anti-malarial drugs artemether, chloroquine, and primaquine, approximately five 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, and metabolomic measurements. The experiment included, 1 pre-inoculation day, 35 experiment days, and 10 post-experiment days. Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively. 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 samples were collected at three time points for functional genomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 24’. This is the second in a series of experiments that includes infection of malaria-naïve subjects (Experiment 23, P. cynomolgi B strain) and heterologous challenge (Experiment 25, P. cynomolgi strain ceylonensis) for the individuals from the same cohort. 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 E24 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 PRJNA408250
Submission date Sep 21, 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 (15)
GSM2789830 2589036_TimePoint1_Whole Blood
GSM2789831 2589055_TimePoint1_Whole Blood
GSM2789832 2589074_TimePoint1_Whole Blood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP118503

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
GSE104101_E24M99FGMmCyXXWB_11022018-Readme_MULTIPL_GEO.txt 17.1 Kb (ftp)(http) TXT
GSE104101_E24M99FGMmCyXXWB_Analytical-Metadata_MULTIPL.xlsx 33.1 Kb (ftp)(http) XLSX
GSE104101_E24M99FGMmCyXXWB_Cynomolgi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 456.9 Kb (ftp)(http) XLSX
GSE104101_E24M99FGMmCyXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 1.8 Mb (ftp)(http) XLSX
GSE104101_E24M99MEMmCyXXWB_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 194.9 Kb (ftp)(http) PDF
GSE104101_E24M99MEMmCyXXWB_Supporting-Clinical-Information_MULTIPL.pdf 172.8 Kb (ftp)(http) PDF
GSE104101_E24M99YSMmCyXXWB_11022018-Readme_MULTIPL_GEO.txt 16.8 Kb (ftp)(http) TXT
GSE104101_E24M99YSMmCyXXWB_11042016-Analytical-Metadata_MULTIPL.xlsx 56.8 Kb (ftp)(http) XLSX
GSE104101_FxGen_read-mapping-and-data-processing_V2.0.pdf 36.3 Kb (ftp)(http) PDF
GSE104101_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE104101_YS_SOP_E24_ClontechV4_SingleCell_cDNASynthesis.pdf 123.5 Kb (ftp)(http) PDF
GSE104101_YS_SOP_E24_Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE104101_nextera-xt-library-prep-protocol-guide-1000000006564-00.pdf 282.8 Kb (ftp)(http) PDF
GSE104101_seq_template_v2.1_mahpic_E24FGWB_GEO.xlsx 72.8 Kb (ftp)(http) XLSX
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Processed data is available on Series record

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