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Sample GSM485083 Query DataSets for GSM485083
Status Public on Dec 16, 2009
Title Leupeptine treatment time-point 4,IC50
Sample type RNA
 
Channel 1
Source name Dd2,start 33hpi, 3hr after treatment
Organism Plasmodium falciparum
Characteristics strain: Dd2
treatment group: Leupeptine
time point: 3 hr
Treatment protocol Synchronzied parasite cultures are splitted into proper number flasks (75ml culture/flask). Total number is double number of time points for one experiment. Half flasks are treated with one compound with the final concentration of IC50 or IC90, and half flasks are negative controls. After the treatment of different time points, parasites in each flask were harvested for total RNA isolation and microarray hybridizations.
Growth protocol Laboratory strain 3D7 and Dd2, sorbitol synchronized. Parasites grow in a 2% suspension of purified human RBCs and RPMI 1640 media supplemented with 0.25% Albumax, 2 g/l sodium bicarbonate, 0.1 mM hypoxanthine, 25 mM HEPES (pH 7.4), and 50 μg/l gentamycin, at 37°C, 5% O2, and 6% CO2. The 3D7 parasites for microarray reference pool were mixed with 6 time-series samples (every 8hrs through a 48hr life cycle), harvested from a 6 liter biofermenter synchronized culture.
Extracted molecule total RNA
Extraction protocol RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool 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.
Label Cy5
Label protocol RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool 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.
 
Channel 2
Source name reference pool
Organism Plasmodium falciparum
Characteristics strain: 3D7
Treatment protocol Synchronzied parasite cultures are splitted into proper number flasks (75ml culture/flask). Total number is double number of time points for one experiment. Half flasks are treated with one compound with the final concentration of IC50 or IC90, and half flasks are negative controls. After the treatment of different time points, parasites in each flask were harvested for total RNA isolation and microarray hybridizations.
Growth protocol Laboratory strain 3D7 and Dd2, sorbitol synchronized. Parasites grow in a 2% suspension of purified human RBCs and RPMI 1640 media supplemented with 0.25% Albumax, 2 g/l sodium bicarbonate, 0.1 mM hypoxanthine, 25 mM HEPES (pH 7.4), and 50 μg/l gentamycin, at 37°C, 5% O2, and 6% CO2. The 3D7 parasites for microarray reference pool were mixed with 6 time-series samples (every 8hrs through a 48hr life cycle), harvested from a 6 liter biofermenter synchronized culture.
Extracted molecule total RNA
Extraction protocol RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool 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.
Label Cy3
Label protocol RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool 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.
 
 
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 no additional information
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, Normalization and subsequent filtering for quality control were carried out using NOMAD database (http://derisilab.ucsf.edu). 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).
 
Submission date Dec 14, 2009
Last update date Dec 15, 2009
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
 
Platform ID GPL7493
Series (1)
GSE19468 Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

Data table header descriptions
ID_REF
VALUE log2 normalized signal intensity ratio Cy5/Cy3

Data table
ID_REF VALUE
aPFE0130c_1 -0.454
aPFC0790w_0 -0.415
aPFE0075c_1 0.847
aPFB0190c_3 1.97
aPFC0275w_1 0.97
aPF14_0419_6 0.389
aPFL1005c_0 0.963
aPFI1120c_2 -0.12
aPFB0580w_1 -0.514
aPF13_0234_0 -1.556
aPFL2440w_0 0.422
aPF10_0108_1 0.226
aPFC0780w_4 -0.12
aPF10_0183_3 0.464
aPFF1225c_2 0.669
aMAL7P1.167_0 1.28
aMAL7P1.167_3 1.104
aPFC0180c_0 null
aPFE0855c_1 -0.377
aMAL8P1.25a_0 0.847

Total number of rows: 10416

Table truncated, full table size 192 Kbytes.




Supplementary file Size Download File type/resource
GSM485083.gpr.gz 899.6 Kb (ftp)(http) GPR
Processed data included within Sample table

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