construct: transgenic 3D7 with an active episomal rif promoter hours post invasion (hpi): 30
Treatment protocol
Parasites were synchronized by repeated sorbitol lysis (Lambros and Vanderberg, 1979) to obtain a eight-hour growth window
Growth protocol
Parasites were cultured as described previously (Trager and Jenson, 1978)
Extracted molecule
total RNA
Extraction protocol
Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions
Label
Cy5
Label protocol
Labeling carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.
Parasites were synchronized by repeated sorbitol lysis (Lambros and Vanderberg, 1979) to obtain a eight-hour growth window
Growth protocol
Parasites were cultured as described previously (Trager and Jenson, 1978)
Extracted molecule
total RNA
Extraction protocol
Total RNA extracted using TriReagent (Ambion) following manufacturer's instructions
Label
Cy3
Label protocol
Labeling carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.
Hybridization protocol
Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).
Scan protocol
Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).
Description
3D7/rif TP3
Data processing
Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).
