|
| Status |
Public on Mar 22, 2018 |
| Title |
11C_TP1ART_074048_Cycle1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
P. falciparum, 11C clone, exposed to 900 nM ART for 1hr
|
| Organism |
Plasmodium falciparum |
| Characteristics |
sample type: In vitro culture (derived fromn 3D7 strain), harvested after 1hr of exposure to 900 nM ART (initiated at 10 HPI)
|
| Treatment protocol |
Synchronized parasites were exposed to 900 nM ART for 4 hrs, starting from 10 HPI
|
| Growth protocol |
Synchronized P. falciparum parasites were grown at 1% parasitemia, 2% hematocrit, and synchronized using 5% sorbitol treatment at 4 HPI
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from parasite cultures using TRIZol-Chloroform method as previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| Label |
Cy5
|
| Label protocol |
Equal amounts (4 µg) of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.
|
| |
|
| Channel 2 |
| Source name |
P. falciparum 3D7 RNA reference pool
|
| Organism |
Plasmodium falciparum |
| Characteristics |
sample type: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle
|
| Treatment protocol |
Synchronized parasites were exposed to 900 nM ART for 4 hrs, starting from 10 HPI
|
| Growth protocol |
Synchronized P. falciparum parasites were grown at 1% parasitemia, 2% hematocrit, and synchronized using 5% sorbitol treatment at 4 HPI
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from parasite cultures using TRIZol-Chloroform method as previously described in detail in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| Label |
Cy3
|
| Label protocol |
Equal amounts (4 µg) of sample cDNA and reference cDNA generated from a 3D7 reference strain were labelled with Cy5 and Cy3, respectively, for 4 hours. Labelled products were subsequently purified and hybridized on the microarray chip using the Agilent hybridization system.
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.
|
| Scan protocol |
Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.
|
| Data processing |
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel were accepted. Log2 ratios were background corrected using a normexp method, followed by loess normalization within arrays, and subsequently with quantile normalization between arrays. Post processing was performed using the Linear Models for Microarray (LIMMA) package for R.
|
| |
|
| Submission date |
Mar 21, 2018 |
| Last update date |
Mar 22, 2018 |
| Contact name |
Frances Maureen Casica Rocamora |
| E-mail(s) |
roca0001@e.ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Street address |
60 Nanyang Drive Nanyang Technological University
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11248 |
| Series (1) |
| GSE112149 |
In vitro transcriptomic profiling of P. falciparum under 4 hr artemisinin challenge (900nM), from 10 HPI |
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