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Series GSE104330 Query DataSets for GSE104330
Status Public on Sep 27, 2017
Title Malaria Host Pathogen Interaction Center Experiment 25: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi strain ceylonensis treated with artemether over 5 time points in a 61 day study.
Organisms Macaca mulatta; Plasmodium cynomolgi ceylonensis
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 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, proteomic, and metabolomic measurements. The experiment included, 8 pre-inoculation days, 49 experiment days, and 4 post-experiment days. Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to subjects at the initial peak of infection, if subjects were not able to self-resolve their parasitemias. Peak infection was determined clinically 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 samples were collected at five time points for functional genomic, lipidomic, proteomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 25’. This is the third and final of a series of experiments that includes infection of malaria-naïve subjects (Experiment 23, P. cynomolgi B strain) and homologous challenge (Experiment 24, P. cynomolgi B strain) of individuals from the same cohort. This dataset was produced by 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 E25 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit . 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).
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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
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BioProject PRJNA412382
Submission date Sep 27, 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)
GPL25694 Illumina HiSeq 3000 (Macaca mulatta; Plasmodium cynomolgi ceylonensis)
Samples (25)
GSM2795501 2650296_TimePoint1_Whole Blood
GSM2795502 2650315_TimePoint1_Whole Blood
GSM2795503 2650334_TimePoint1_Whole Blood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
SRA SRP118996

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Supplementary file Size Download File type/resource
GSE104330_E25M99MEMmCyDaWB_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 200.0 Kb (ftp)(http) PDF
GSE104330_E25M99MEMmCyDaZZ_Supporting-Clinical-Information_XXXXXXX.pdf 249.2 Kb (ftp)(http) PDF
GSE104330_E25M99YSMmCyDaWB_110252018-Readme_MULTIPL_GEO.txt 18.6 Kb (ftp)(http) TXT
GSE104330_E25M99YSMmCyDaWB_11042016-Analytical-Metadata_MULTIPL.xlsx 58.0 Kb (ftp)(http) XLSX
GSE104330_E25bM99FGMmCyDaWB_11022018-Readme_MULTIPL_GEO.txt 20.4 Kb (ftp)(http) TXT
GSE104330_E25bM99FGMmCyDaWB_Analytical-Metadata_MULTIPL.xlsx 34.4 Kb (ftp)(http) XLSX
GSE104330_E25bM99FGMmCyDaWB_Cynomolgi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 808.7 Kb (ftp)(http) XLSX
GSE104330_E25bM99FGMmCyDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 2.7 Mb (ftp)(http) XLSX
GSE104330_FxGen_read-mapping-and-data-processing_V2.0.pdf 36.3 Kb (ftp)(http) PDF
GSE104330_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE104330_YS_SOP_E25_ClontechV4_SingleCell_cDNASynthesis.pdf 123.5 Kb (ftp)(http) PDF
GSE104330_YS_SOP_E25_Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE104330_nextera-xt-library-prep-protocol-guide-1000000006564-00.pdf 282.8 Kb (ftp)(http) PDF
GSE104330_seq_template_v2.1_mahpic_E25FGWB_GEO.xlsx 79.3 Kb (ftp)(http) XLSX
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