|
| Status |
Public on Jun 01, 2016 |
| Title |
3D7_ART_6 hours_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
3D7_ART_6 hours_2
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture: In vitro culture
laboratory strain: 3D7
Stage: asexual blood stage: trophozoite
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions and as described 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 |
Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described 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.
|
| |
|
| Channel 2 |
| Source name |
P. falciparum 3D7 RNA reference pool
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture: In vitro culture
Stage: asexual blood stage
laboratory strain: 3D7
composition: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions and as described 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 |
Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described 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.
|
| |
|
| |
| Hybridization protocol |
Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.
|
| Scan protocol |
The microarrays were scanned using GenePix scanner 400b. 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 passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.
|
| |
|
| Submission date |
Sep 01, 2015 |
| Last update date |
Jun 01, 2016 |
| Contact name |
Devendra Kumar Gupta |
| E-mail(s) |
devendra1@e.ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
ZB Lab
|
| Street address |
60 NANYANG DRIVE
|
| City |
singapore |
| State/province |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11248 |
| Series (2) |
| GSE72578 |
DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. [RNA] |
| GSE72580 |
DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. |
|
