 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 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
|
| |
|
| 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 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).
|
| Web link |
http://www.systemsbiology.emory.edu/index.htmlhttp://plasmodb.org/plasmo/mahpic.jsp
|
| |
|
| 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 |
| GSM3019588 |
9993000004_RingStage(A+)_Cultured Cells |
| GSM3019589 |
9993000005_RingStage(B+1+)_Cultured Cells |
| GSM3019590 |
9993000006_RingStage(C+)_Cultured Cells |
| GSM3019591 |
9993000007_RingStage(A+)_Cultured Cells |
| GSM3019592 |
9993000008_RingStage(B+1+)_Cultured Cells |
| GSM3019593 |
9993000009_RingStage(C+)_Cultured Cells |
|
| This SubSeries is part of SuperSeries: |
| GSE94274 |
An Integrated Approach to Understanding Host-Pathogen Interactions |
|
| Relations |
| SRA |
SRP189666 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...