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Series GSE127079 Query DataSets for GSE127079
Status Public on Mar 01, 2019
Title Malaria Host Pathogen Center Experiment 06: Macaca mulatta infected with Plasmodium knowlesi sporozoites to produce and integrate clinical, hematological, parasitological, omics, telemetric, and histopathological measures of acute primary infection.
Organisms Plasmodium knowlesi; Macaca mulatta
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 has continued with 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.
 
Overall design Telemetry devices (DSI, model L11) with blood pressure sensors and electrocardiogram (ECG) leads were surgically implanted in four malaria-naive male rhesus macaques (Macaca mulatta), approximately five years of age. After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected. Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved P. knowlesi Malayan strain salivary gland sporozoites, obtained from Anopheles dirus infected with parasites from the Pk1A+ clone and previously tested in E30 for their infectivity of macaques. The sporozoite stocks used were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention, and then stored at Yerkes. After inoculation, the macaques were profiled longitudinally for clinical, hematological, parasitological, immunological, functional genomic, proteomic, and metabolomic measurements. The experiment was designed with pathology studies and thus terminal necropsies, which were scheduled at the log phase of the infections or at the peak of parasitemias. Capillary blood samples were collected daily for the measurement of complete blood counts, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomics analyses. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, targeted proteomic, targeted metabolomics, and immunological analyses. Physiological data noted above were continuously captured via the implanted telemetry devices. Within the MaHPIC, this project is known as ‘Experiment 06’. 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 E06 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) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).
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, Lackman N, Lapp SA, Moreno A, Nural M, Pakala SB, Patel N, Joyner CJ, Peterson MS, Tharp GK, Jiang J, Gutierrez JB, Tirouvanziam RM
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA524357
Submission date Feb 25, 2019
Last update date Apr 22, 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)
GPL25695 Illumina HiSeq 3000 (Macaca mulatta; Plasmodium knowlesi)
Samples (47)
GSM3625499 3118700_Bone Marrow_2
GSM3625500 3151100_Bone Marrow_Necropsy
GSM3625501 3107086_Whole blood_TimePoint1
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP186947

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
GSE127079_E06E30_Knowlesi-Normalized-Samples-06132018.xlsx 57.8 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXBM_Analytical-Metadata_MULTIPL.xlsx 55.9 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXBM_ERCC-Controls-RawCounts-Results_MULTIPL_GEO.xlsx 26.7 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXBM_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 600.7 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXBM_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 2.4 Mb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXSP_Analytical-Metadata_MULTIPL.xlsx 39.4 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXSP_ERCC-Controls-RawCounts-Results_MULTIPL_GEO.xlsx 15.9 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXSP_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 229.7 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXSP_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 851.5 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXWB_Analytical-Metadata_MULTIPL.xlsx 55.1 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXWB_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 571.2 Kb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXWB_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 2.3 Mb (ftp)(http) XLSX
GSE127079_E06M99FGMmKnXXZZ_06292018-Readme_MULTIPL_GEO.txt 19.1 Kb (ftp)(http) TXT
GSE127079_E06M99FGMmKnXxWB_ERCC-Controls-RawCounts-Results_MULTIPL_GEO.xlsx 25.9 Kb (ftp)(http) XLSX
GSE127079_E06M99MEMmKnXXZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 584.5 Kb (ftp)(http) PDF
GSE127079_E06M99MEMmKnXXZZ_Supporting-Clinical-Information_MULTIPL.pdf 179.0 Kb (ftp)(http) PDF
GSE127079_E06M99YSMmKnXXBM_10042017-Analytical-Metadata-BoneMarrow_MULTIPL.xlsx 39.7 Kb (ftp)(http) XLSX
GSE127079_E06M99YSMmKnXXZZ_06082018-Readme_MULTIPL_GEO.txt 16.2 Kb (ftp)(http) TXT
GSE127079_E06M99YSMmKnXXZZ_10042017-Analytical-Metadata-WholeBlood-Spleen_MULTIPL.xlsx 41.6 Kb (ftp)(http) XLSX
GSE127079_E99M99FGMmKnDaBM_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 7.8 Mb (ftp)(http) XLSX
GSE127079_E99M99FGMmKnDaSP_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 1.7 Mb (ftp)(http) XLSX
GSE127079_E99M99FGMmKnDaWB_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 7.4 Mb (ftp)(http) XLSX
GSE127079_E99NecFGMmKnXXZZ_E06-E30-WBvsNec-Knowlesi-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 875.0 Kb (ftp)(http) XLSX
GSE127079_E99T99FGMmKnXXWB_E06-E30-WB-TP4vsTP5-Knowlesi-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 663.3 Kb (ftp)(http) XLSX
GSE127079_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE127079_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE127079_FxGen_read-mapping-and-data-processing_V2.1.pdf 55.9 Kb (ftp)(http) PDF
GSE127079_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE127079_SOP71.1__Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE127079_SOP_69.1_Spike-inERCC_Controls.pdf 126.1 Kb (ftp)(http) PDF
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