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| Status |
Public on Jun 01, 2017 |
| Title |
Malaria Host Pathogen Interaction Center Experiment 04: 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
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| 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).
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| Overall design |
Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, 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 to three 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 of malaria. The anti-malarial drugs chloroquine and primaquine were administered to all remaining subjects at the end of the study for curative treatment of the liver- and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and at seven-time points from venous blood. The seven-time point collections were used to generate these results. This dataset was generated from whole blood samples from 5 individuals collected 7 times over the 100-day experiment. Since one animal was euthanized after time point 3 (meaning 4 potential samples were not collected from this animal, 2 samples failed library preparation, and one sample was collected from a blood transfusion donor animal, a total of 30 samples were collected. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04). To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics data sets, please visit http://plasmodb.org/plasmo/mahpic.jsp .
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| Web link |
http://www.systemsbiology.emory.edu/index.html http://plasmodb.org/plasmo/mahpic.jsp
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| Contributor(s) |
Arafat D, Bosinger S, Cabrera M, DeBarry JD, Galinski M, Garimalla S, Humphrey J, Karpuzoglu E, Kissinger JC, Lapp S, Lee K, Joice R, Joyner C, Meyer E, Moreno A, Nayak V, Nural M, Pakala S, Patel N, Tang Y, Tharp G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA388645 |
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| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary Galinski |
| Organization name |
Emory University
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| Department |
Vaccine Center at Yerkes
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| Lab |
Galinski Lab
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| Street address |
954 Gatewood Road
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
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| Platforms (1) |
| GPL25692 |
Illumina HiSeq 2000 (Macaca mulatta; Plasmodium cynomolgi strain B) |
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| Samples (30)
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| This SubSeries is part of SuperSeries: |
| GSE94274 |
An Integrated Approach to Understanding Host-Pathogen Interactions |
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| Relations |
| SRA |
SRP108356 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99486_E04M99FGMmCyDaWB_Cynomolgi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx |
1.3 Mb |
(ftp)(http) |
XLSX |
| GSE99486_E04M99FGMmCyDaWB_IFX-11012018-RNA-Seq-Readme_MULTIPL_GEO.txt |
27.0 Kb |
(ftp)(http) |
TXT |
| GSE99486_E04M99FGMmCyDaWB_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx |
4.6 Mb |
(ftp)(http) |
XLSX |
| GSE99486_E04M99FGMmCyDaZZ_Experiment-Summary-Diagram-Supplementary_XXXXXXX.pdf |
78.3 Kb |
(ftp)(http) |
PDF |
| GSE99486_E04M99FGMmDaCyWB_01232017-Analytical-Metadata_MULTIPL.xlsx |
215.0 Kb |
(ftp)(http) |
XLSX |
| GSE99486_E04M99MEMmCyDaZZ_Supporting-Clinical-Information_XXXXXXX.pdf |
230.8 Kb |
(ftp)(http) |
PDF |
| GSE99486_E04M99YSMmDaCyWB_Samples-1-30-IFX-Readme-11012018_MULTIPL_GEO.txt |
13.9 Kb |
(ftp)(http) |
TXT |
| GSE99486_EN-RNeasy-Plus-Mini-Handbook_Qiagen_Sep2010_GEO.pdf |
661.1 Kb |
(ftp)(http) |
PDF |
| GSE99486_Extraction_Whole_Blood_AppliedBiosystems_Part4329232RevD.pdf |
376.0 Kb |
(ftp)(http) |
PDF |
| GSE99486_FxGen_RNAextractionWholeBlood_v1_Mar13_2013.pdf |
463.5 Kb |
(ftp)(http) |
PDF |
| GSE99486_FxGen_read-mapping-normalization-and-data-analysis_v1.4_28August2014_GEO.pdf |
214.0 Kb |
(ftp)(http) |
PDF |
| GSE99486_MaHPIC_File_Naming_Standards_2_23_2018.pdf |
96.4 Kb |
(ftp)(http) |
PDF |
| GSE99486_RNA_Extraction_SOP_Mar_13_2013_GEO.pdf |
228.0 Kb |
(ftp)(http) |
PDF |
| GSE99486_seq_template_v2.1_mahpic_E04FGWB.xls.gz |
29.0 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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