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Series GSE19468 Query DataSets for GSE19468
Status Public on Dec 16, 2009
Title Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum
Organism Plasmodium falciparum
Experiment type Expression profiling by array
Summary The microarray experiments were carried out using a long oligonucleotide DNA microarray that represent all 5363 P. falciparum genes with one oligonucleotide per 1.9kb of coding sequence on average (Hu et al. 2007). Total 247 microarray experiments were carried out including 29-drug treatment time courses with 20 compounds and corresponding untreated controls from different drug or inhibitor treatment. Data of each drug/inhibitor experiment were normalized using a linear normalization and background filtering as implemented by the NOMAD database (http://derisilab.ucsf.edu).
 
Overall design Time-series sampling and experiments with synchronized ex vivo culturing parasites. Each experiment has treatment and controls, and starts at a specific time of post invasion. For an example of quinine treatment, the treatments start from late ring stage through trophozoite stage of the parasites. First, IC50 is determined by drug assay with synchronized parasites (5% parasiteomia and 2% RBC). Second, synchronized parasite cultures are splitted into 12 flasks (75ml culture/flask) for a 6 time-point time-series experiment. 6 flasks are treated with quinine (final concentration is IC50) and 6 flasks are negative controls. 1,2,4,6,8 and 10 hrs after the treatment, parasites in each flask were harvested for total RNA isolation and microarray hybridizaiton.
 
Contributor(s) Hu G, Mok S, Chaal BK, Bozdech Z
Citation(s) 20037583
Submission date Dec 14, 2009
Last update date Aug 08, 2013
Contact name Guangan Hu
E-mail(s) hu0002an@ntu.edu.sg
Phone 65 63162926
Fax 65 63162801
Organization name Nanyang Technological Unversity
Department School of biological sciences
Lab Malaria
Street address 60 Nanyang Drive
City Singapore
ZIP/Postal code 637551
Country Singapore
 
Platforms (1)
GPL7493 ZB/SBS-NTU Plasmodium falciparum 3D7 10.4K v1.0
Samples (247)
GSM484919 Control time-point 1 for ML7/W7/KN7/Staurosporine1
GSM484920 Control time-point 2 for ML7/W7/KN7/Staurosporine1
GSM484921 Control time-point 3 for ML7/W7/KN7/Staurosporine1
Relations
BioProject PRJNA120341

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
GSE19468_RAW.tar 210.9 Mb (http)(custom) TAR (of GPR)
Raw data provided as supplementary file
Processed data included within Sample table

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