P. falciparum cells were sorbitol synchronized and grown up to 10-15% parasetemia in 2% hematocrit. Wild type cells were harvested either directly for RNA extraction or after drug treatment. Transfected cells were grown in media supplemented with Blasticidin
Extracted molecule
total RNA
Extraction protocol
RNA extraction was carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.
Label
Cy5
Label protocol
Labeling carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.
control type: Reference pool consisting of RNA from 6 time points across 3D7 parental strain
Treatment protocol
P. falciparum cells were sorbitol synchronized and grown up to 10-15% parasetemia in 2% hematocrit. Wild type cells were harvested either directly for RNA extraction or after drug treatment. Transfected cells were grown in media supplemented with Blasticidin
Extracted molecule
genomic DNA
Extraction protocol
RNA extraction was carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.
Label
Cy3
Label protocol
Labeling carried out as described in Bozdech, Z., Llinas, M., Pulliam, B.L., Wong, E.D., Zhu, J., and DeRisi, J.L. (2003). The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.
Hybridization protocol
Hybridizations were performed on the Agilent hybridization system for 20 h
Scan protocol
Microarray scanning was done using PowerScanner (Tecan, Austria)
Data processing
Data was processed using Limma Package of R (Edwards, D. (2003). Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics 19, 825-833). . Briefly, lowess normalization was applied to all spots on each array followed by quantile normalization between arrays. Spots with flag >0 and median foreground intensity >1.5-fold median background intensity for either channel were included. The normalized log2 ratio of Cy5 versus Cy3 channel was used to present the fold change.
