sample type: ChIP with anti-H3K4me3 from time point 4 (40 hpi) chip antibody: anti-H3K4me3 time: 40 hpi tissue: whole organism
Treatment protocol
P. falciparum cells were harvested at 5% parasetemia in 2% hematocrit either directly for RNA extraction or saponin lysed and formaldehyde cross linked for immuno-precipitation
Extracted molecule
genomic DNA
Extraction protocol
Chromatin-immuno precipitation and RNA extraction was carried out as described in Gupta AP, ChIn WH, Zhu L, Bozdech Z: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life
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.
sample type: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6 tissue: whole organism
Treatment protocol
P. falciparum cells were harvested at 5% parasetemia in 2% hematocrit either directly for RNA extraction or saponin lysed and formaldehyde cross linked for immuno-precipitation
Extracted molecule
genomic DNA
Extraction protocol
Chromatin-immuno precipitation and RNA extraction was carried out as described in Gupta AP, ChIn WH, Zhu L, Bozdech Z: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life
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).
Data processing
Data was Lowess normailzed and further processed as described in Gupta AP, Hoe CW, Lei Z, Bozdech Z: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life cycle (manuscript in prep.)
