E-GEOD-14524 - Transcriptomic and metabolomic profiles of the Plasmodium falciparum developmental cycle

Status
Submitted on 22 January 2009, released on 23 January 2009, last updated on 1 May 2014
Organism
Plasmodium falciparum, Plasmodium falciparum (3D7)
Samples (14)
Array (1)
Protocols (27)
Description
In order to further our understanding of the metabolic network of the malaria parasite, Plasmodium falciparum, we carried out a concurrent transcriptomic and metabolomic study of the parasite's intraerythrocytic developmental cycle. These microarray data were generated to compare the expression levels of metabolic enzymes to the concentrations of their associated metabolites over the 48-hour life cycle. Sorbitol-synchronized Plasmodium falciparum (3D7 strain) was grown in tissue culture flasks in incubators according to standard protocols. Immediately after reinvasion, and at 8-hour intervals thereafter, parasites were harvested by centrifugation. For each timepoint, 0.5 mL of packed RBC (10% parasitemia) was pelleted by centrifugation, washed once in PBS and flash-frozen in liquid nitrogen. Total RNA isolation and amino-allyl cDNA labeling were as previously described (Bozdech et al., 2003). A pool of 3D7 total RNA from all intraerythrocytic developmental stages was generated and used as the reference sample. For DNA microarray hybridization, pool cDNA was coupled to Cy3 dye, while cDNA from an individual timepoint was coupled to Cy5 dye. DNA microarrays were scanned using an Axon 4200A scanner and images analyzed using Axon GenePix software (Axon Instruments, Union City, CA, USA). Microarray data were stored and analyzed using our in-house database PUMAdb (Princeton University MicroArray database). All data for individual arrays were normalized by a global normalization using unflagged features with >= 65% of pixels one or more standard deviations over local background. All unflagged spots were selected and extracted for further analysis. Data were filtered to remove oligos more than 1 datapoint missing across the timeseries, log2 transformed, mean centered, ordered by the timing of their peak expression level, and visualized with Java Treeview (Saldanha, 2004) (Table S3).
Experiment type
transcription profiling by array 
Contacts
Kellen Olszewski <kolszews@princeton.edu>, Akhil B Vaidya, Daniel Wilinski, James M Burns, Joanne M Morrisey, Joshua D Rabinowitz, Kellen L Olszewski, Manuel Llinás
Citation
Host-parasite interactions revealed by Plasmodium falciparum metabolomics. Olszewski KL, Morrisey JM, Wilinski D, Burns JM, Vaidya AB, Rabinowitz JD, Llinás M.
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-14524.idf.txt
Sample and data relationshipE-GEOD-14524.sdrf.txt
Raw data (1)E-GEOD-14524.raw.1.zip
Processed data (1)E-GEOD-14524.processed.1.zip
Array designA-GEOD-8088.adf.txt
R ExpressionSetE-GEOD-14524.eSet.r
Links