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Series GSE123495 Query DataSets for GSE123495
Status Public on Feb 25, 2019
Title Malaria Host Pathogen Interaction Center Experiment 30: Pilot experiment for Macaca mulatta infected with Plasmodium knowlesi Malayan strain sporozoites to produce and integrate 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 two malaria-naive male rhesus macaques (Macaca mulatta), approximately three 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. The P. knowlesi sporozoites were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention. After inoculation, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, metabolomic, telemetric and histopathological measurements. The experiment was designed for pathology studies, with terminal necropsies on days 11 (RKy15) or 19 (Red16). The anti-malarial drug artemether was subcuratively administered selectively to one subject (REd16) during the primary parasitemia to suppress clinical complications. 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 metabolomic analysis. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, proteomic, lipidomic, and immunological analyses. Physiological data were continuously captured via telemetry. Within the MaHPIC, this project is known as â??Experiment 30â??. This dataset was produced by Steven E Bosinger, Nirav Patel, and Gregory K Tharp at Emory University. To access other publicly available results from E30 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).The MaHPIC Consortium
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, Gutierrez JB, Tirouvanziam RM
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA508940
Submission date Dec 07, 2018
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 (63)
GSM3505066 2927581_Whole-blood-Venous_TimePoint1
GSM3505067 2927595_Whole-blood-Capillary_TimePoint1
GSM3505068 2927599_Bone-Marrow_TimePoint1
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP173197

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
GSE123495_E06E30_Knowlesi-Normalized-Samples-06132018.xlsx 57.8 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaBM_Analytical-Metadata-PAXgene_MULTIPL.xlsx 53.2 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaBM_ERCC-Controls-RawCounts-Results_MULTIPL-GEO.xlsx 44.4 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaBM_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 396.8 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaBM_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 1.6 Mb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaSP_Analytical-Metadata-RNALater_MULTIPL.xlsx 33.9 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaSP_ERCC-Controls-RawCounts-Results_MULTIPL-GEO.xlsx 43.1 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaSP_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 198.4 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaSP_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 676.7 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWB_Analytical-Metadata-PAXgene_MULTIPL.xlsx 53.2 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWB_ERCC-Controls-RawCounts-Results_MULTIPL-GEO.xlsx 44.6 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWB_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 399.0 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx 1.6 Mb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWC_Analytical-Metadata-RNAProtect_MULTIPL.xlsx 55.8 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWC_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 849.0 Kb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWC_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 8.4 Mb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaWC_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 3.9 Mb (ftp)(http) XLSX
GSE123495_E30M99FGMmKnDaZZ_02222019-Readme_MULTIPL-GEO.txt 21.6 Kb (ftp)(http) TXT
GSE123495_E30M99MEMmKnDaZZ_Supporting-Clinical-Information_MULTIPL.pdf 521.8 Kb (ftp)(http) PDF
GSE123495_E30M99YSMmKnDaSP_02222019-ReadmeRNALater_MULTIPL-GEO.txt 15.4 Kb (ftp)(http) TXT
GSE123495_E30M99YSMmKnDaSP_10162017-Analytical-Metadata-Spleen_MULTIPL.xlsx 31.0 Kb (ftp)(http) XLSX
GSE123495_E30M99YSMmKnDaZZ_02222019-ReadmePaxgene_MULTIPL-GEO.txt 17.4 Kb (ftp)(http) TXT
GSE123495_E30M99YSMmKnDaZZ_02222019-ReadmeRNAProtect_MULTIPL-GEO.txt 19.2 Kb (ftp)(http) TXT
GSE123495_E30M99YSMmKnDaZZ_05232017-Analytical-Metadata-Paxgene_MULTIPL.xlsx 94.6 Kb (ftp)(http) XLSX
GSE123495_E30M99YSMmKnDaZZ_05232017-Analytical-Metadata-RNAProtectRun1_MULTIPL.xlsx 95.6 Kb (ftp)(http) XLSX
GSE123495_E30M99YSMmKnDaZZ_05232017-Analytical-Metadata-RNAProtectRun2_MULTIPL.xlsx 93.8 Kb (ftp)(http) XLSX
GSE123495_E30M99YSMmKnDaZZ_Experiment-Summary-Diagram-Supplementary_MULTIPL.pdf 67.3 Kb (ftp)(http) PDF
GSE123495_E99M99FGMmKnDaBM_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 7.8 Mb (ftp)(http) XLSX
GSE123495_E99M99FGMmKnDaSP_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 1.8 Mb (ftp)(http) XLSX
GSE123495_E99M99FGMmKnDaWB_Mulatta-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 7.4 Mb (ftp)(http) XLSX
GSE123495_E99NecFGMmKnXXZZ_E06-E30-WBvsNec-Knowlesi-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 897.0 Kb (ftp)(http) XLSX
GSE123495_E99T99FGMmKnXXWB_E06-E30-WB-TP4vsTP5-Knowlesi-Genes-DESeq2NormalizedCounts-Results_MULTIPL-GEO.xlsx 675.1 Kb (ftp)(http) XLSX
GSE123495_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE123495_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE123495_FxGen_read-mapping-and-data-processing_V2.1.pdf 55.9 Kb (ftp)(http) PDF
GSE123495_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE123495_SOP71.1__Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE123495_SOP_69.1_Spike-inERCC_Controls.pdf 126.1 Kb (ftp)(http) PDF
GSE123495_YS_SOP_E30_ClontechV4_SingleCell_cDNASynthesis.pdf 123.5 Kb (ftp)(http) PDF
GSE123495_YS_SOP_E30_Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE123495_nextera-xt-library-prep-protocol-guide-1000000006564-00.pdf 282.8 Kb (ftp)(http) PDF
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