NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE103507 Query DataSets for GSE103507
Status Public on Sep 07, 2017
Title Malaria Host Pathogen Interaction Center Experiment 04R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi 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 three 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 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs primaquine and chloroquine were administered to all remaining 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. Within the MaHPIC, this project is known as ‘Experiment 04R’. 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 E04R 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. E04R is a 'resequencing' of the same samples from E04. Resequencing for E04R was processed with SOPs and technology consistent with that used for E23R, E24, and E25 so that results from these experiments could be reliably compared. E04R does not replace E04, these are distinct datasets. Relative to E04, E04R is only for MaHPIC Yerkes Sequencing and Functional Genomics results. Only E04R is intended for comparison with E23R, E24, and E25.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) Arafat D, Bosinger SS, Cabrera-Mora M, DeBarry JD, Galinski MR, Humphrey JC, Karpuzoglu E, Kissinger JC, Lapp SA, Joice-Cordy R, Joyner CJ, Meyer EV, Moreno A, Nayak V, Nural M, Pakala SB, Patel N, Tang Y, Tharp G
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA401436
Submission date Sep 05, 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 (33)
GSM2772556 2063483_TimePoint7_WholeBlood
GSM2772557 2063484_TimePoint6_WholeBlood
GSM2772558 2063485_TimePoint7_WholeBlood
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
Relations
SRA SRP116793

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
GSE103507_E04M99MEMmCyDaZZ_Supporting-Clinical-Information_XXXXXXX.pdf 230.8 Kb (ftp)(http) PDF
GSE103507_E04RM99FGMmCyDaWB_11022018-Readme_MULTIPL_GEO.txt 20.5 Kb (ftp)(http) TXT
GSE103507_E04RM99FGMmCyDaWB_Analytical-Metadata_MULTIPL.xlsx 48.4 Kb (ftp)(http) XLSX
GSE103507_E04RM99FGMmCyDaWB_Cynomolgi-Genes-RawCountsReSequence-Results_MULTIPL_GEO.xlsx 1.0 Mb (ftp)(http) XLSX
GSE103507_E04RM99FGMmCyDaWB_ERCC-Controls-RawCountsReSequence-Results_MULTIPL.xlsx 45.9 Kb (ftp)(http) XLSX
GSE103507_E04RM99FGMmCyDaWB_Mulatta-Genes-DESeq2NormalizedCountsReSequence-Results_MULTIPL_GEO.xlsx 7.5 Mb (ftp)(http) XLSX
GSE103507_E04RM99FGMmCyDaWB_Mulatta-Genes-RawCountsReSequence-Results_MULTIPL.xlsx 3.6 Mb (ftp)(http) XLSX
GSE103507_E04RM99FGMmCyDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf 78.3 Kb (ftp)(http) PDF
GSE103507_E04RM99YSMmCyDaWB_05252017-Analytical-Metadata-Run1_MULTIPL.xlsx 34.0 Kb (ftp)(http) XLSX
GSE103507_E04RM99YSMmCyDaWB_05252017-Analytical-Metadata-Run2_MULTIPL.xlsx 34.0 Kb (ftp)(http) XLSX
GSE103507_E04RM99YSMmCyDaWB_11022018-Readme_MULTIPL_GEO.txt 18.8 Kb (ftp)(http) TXT
GSE103507_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE103507_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE103507_FxGen_read-mapping-and-data-processing_V2.1.pdf 52.8 Kb (ftp)(http) PDF
GSE103507_MaHPIC_File_Naming_Standards_2_23_2018.pdf 96.4 Kb (ftp)(http) PDF
GSE103507_YS_SOP_E04R_ClontechV4_SingleCell_cDNASynthesis.pdf 123.5 Kb (ftp)(http) PDF
GSE103507_YS_SOP_E04R_Illumina_TruSeqRNA_mRNA_Stranded.pdf 201.9 Kb (ftp)(http) PDF
GSE103507_nextera-xt-library-prep-protocol-guide-1000000006564-00.pdf 282.8 Kb (ftp)(http) PDF
GSE103507_seq_template_v2.1_mahpic_E04RFGWB_GEO.xls.gz 65.5 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap