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Series GSE108034 Query DataSets for GSE108034
Status Public on Dec 18, 2017
Title Ex vivo P. falciparum from High vs Low transmission areas in east Africa
Organism Plasmodium falciparum
Experiment type Expression profiling by array
Summary The aim of this study was to compare the transcriptomes of Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment. In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and measured for gene expression levels by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Rono MK, Nyonda MA, Simam JJ, Ngoi, JM et al. Nat Ecol Evol. PMID: .
 
Overall design 515 samples were analysed. These derived from 96 parasite isolates obtained from children below 13 years of age with three or fewer previous clinical episodes of malaria who were diagnosed with uncomplicated P. falciparum malaria at hospitals and dispensaries in western Kenya (2008, Kisumu), coastal Kenya (Kilifi, in 1994-1996 and in 2010-2012) and eastern Sudan (2007) which have long-term high, medium and low malaria transmission intensities, respectively. Each isolate was placed into in vitro culture and sampled every 10h for up to 9 times: this yielded parasites at all stages of maturity during the 48h intraerythrocytic development cycle. Five of the 96 isolates were replicates but were processed separately.
 
Contributor(s) Mackinnon MJ, Rono MK
Citation(s) 29255304
Submission date Dec 13, 2017
Last update date Mar 19, 2018
Contact name Margaret Jane Mackinnon
Organization name None
Street address None
City None
State/province None
ZIP/Postal code 1111
Country Australia
 
Platforms (3)
GPL24385 ZB/SBS-NTU Plasmodium falciparum 3D7 IGR + ORF 16.4k v1.0
GPL24386 ZB/SBS-NTU Plasmodium falciparum 3D7 11.0k v1.1
GPL24387 ZB/SBS-NTU Plasmodium falciparum 3D7 11.4K v1.2
Samples (515)
GSM2887792 ex-vivo_culture_timepoint_1_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T1
GSM2887793 ex-vivo_culture_timepoint_2_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T2
GSM2887794 ex-vivo_culture_timepoint_3_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T3
Relations
BioProject PRJNA422261

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
GSE108034_RAW.tar 600.1 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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