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Series GSE110970 Query DataSets for GSE110970
Status Public on Feb 22, 2019
Title Malaria Host Pathogen Interaction Center Experiment S01: Host and parasite gene transcript abundances, from cultured cells, of Macaca mulatta infected with Plasmodium knowlesi Pk1(A+), Pk1(B+)1+, Pk1(C+) ex vivo time course.
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) - is 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
Overall design Malaria-naive rhesus macaques (Macaca mulatta), were inoculated with a particular parasite clone and allowed to reach a targeted peak parasitemia of 5% - 10% proportion of infected RBCs. Whole blood was collected at the early ring stage while subjects were under anesthesia, and an ex vivo culture was established using standard protocols, which include but are not limited to the processing of the whole blood by removing platelets and white blood cells. Samples were collected starting at 1.5-2 hours after establishing cultures, followed by collections every 4 hours for a 24 hour period. Blood-stage curative doses of the anti-malarial drug chloroquine were administered to all subjects after whole blood extraction from each subject. Parasitemias were monitored daily by earsticks. Within the MaHPIC, this project is known as ‘Supporting Project 01’. 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 'S01' including proteomics and other MaHPIC Experiments, 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).
Web link
Contributor(s) Bosinger SE, DeBarry JD, Galinski MR, Hankus A, Kissinger JC, Lackman N, Lapp SA, Nural M, Patel N, Peterson MS, Tharp GK
Citation(s) 30096152
BioProject PRJNA435509
Submission date Feb 21, 2018
Last update date May 24, 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 (9)
GSM3019585 9993000001_RingStage(A+)_Cultured Cells
GSM3019586 9993000002_RingStage(B+1+)_Cultured Cells
GSM3019587 9993000003_RingStage(C+)_Cultured Cells
This SubSeries is part of SuperSeries:
GSE94274 An Integrated Approach to Understanding Host-Pathogen Interactions
SRA SRP189666

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE110970_ERCC92.fa.gz 26.1 Kb (ftp)(http) FA
GSE110970_ERCC92.gtf.gz 1.1 Kb (ftp)(http) GTF
GSE110970_Ex_vivo_prep_of_RBCs.pdf 51.0 Kb (ftp)(http) PDF
GSE110970_FxGen_read-mapping-and-data-processing_V2.1.pdf 54.4 Kb (ftp)(http) PDF
GSE110970_Illumina_TruSeq_Stranded_TotalRNA_SamplePrep_Guide_15031048_C.pdf 4.9 Mb (ftp)(http) PDF
GSE110970_MaHPIC_File_Naming_Standards_1_18_2018.pdf 82.5 Kb (ftp)(http) PDF
GSE110970_RPMI_recipe.pdf 30.8 Kb (ftp)(http) PDF
GSE110970_S01XXXFGMmKnXXCC_01082018-RingStage-Readme_MULTIPL_GEO.txt 12.8 Kb (ftp)(http) TXT
GSE110970_S01XXXFGMmKnXXCC_RingStage-Analytica-Metadata_MULTIPL.xlsx 48.2 Kb (ftp)(http) XLSX
GSE110970_S01XXXFGMmKnXXCC_RingStage_ERCC-Controls-RawCounts-Results_MULTIPL_GEO.xlsx 37.8 Kb (ftp)(http) XLSX
GSE110970_S01XXXFGMmKnXXCC_RingStage_Knowlesi-Genes-DESeq2NormalizedCounts-Results_MULTIPL_GEO.xlsx 803.8 Kb (ftp)(http) XLSX
GSE110970_S01XXXFGMmKnXXCC_RingStage_Knowlesi-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 431.7 Kb (ftp)(http) XLSX
GSE110970_S01XXXFGMmKnXXCC_RingStage_Mulatta-Genes-RawCounts-Results_MULTIPL_GEO.xlsx 1.1 Mb (ftp)(http) XLSX
GSE110970_S01XXXYSMmKnXXCC_01082018-RingStage-Readme_MULTIPL_GEO.txt 13.4 Kb (ftp)(http) TXT
GSE110970_S01XXXYSMmKnXXCC_RingStage-Analytical-Metadata_MULTIPL.xlsx 50.7 Kb (ftp)(http) XLSX
GSE110970_S01XXXYSMmKnXXCC_RingStage-AssayDetails_MULTIPL.xlsx 23.2 Kb (ftp)(http) XLSX
GSE110970_SOP_69.1_Spike-inERCC_Controls.pdf 126.1 Kb (ftp)(http) PDF
GSE110970_Total_RNA_Extraction_from_Parasite_Cultures.pdf 53.9 Kb (ftp)(http) PDF
GSE110970_seq_template_v2.1_mahpic_S01FGCC_GEO.xlsx 70.6 Kb (ftp)(http) XLSX
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Processed data are available on Series record

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