|
| Status |
Public on Nov 24, 2015 |
| Title |
ChIPm1/2m16 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ls -1 myc16_0635.gpr
|
| Organism |
Plasmodium falciparum |
| Characteristics |
genotype/variation: transgenic 3D7 with over-expression of PfZnFP-G
|
| 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 |
genomic DNA |
| 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.
|
| |
|
| Channel 2 |
| Source name |
input DNA before immunoprecipitation
|
| Organism |
Plasmodium falciparum |
| Characteristics |
genotype/variation: transgenic 3D7 with over-expression of PfZnFP-G
|
| 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 |
genomic DNA |
| 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_over-expression_16 hpi
|
| 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).
|
| |
|
| Submission date |
Nov 23, 2015 |
| Last update date |
Nov 24, 2015 |
| Contact name |
Yen-Hoon Luah |
| E-mail(s) |
yanfenlai@gmail.com
|
| Organization name |
Nanyang Technological University
|
| Street address |
Nanyang Technological University 60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11250 |
| Series (1) |
| GSE75295 |
A crucial role of the zinc finger protein PfZnFP-G in sexual differentiation of the malaria parasites, Plasmodium falciparum |
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