|
| Status |
Public on Feb 07, 2013 |
| Title |
clone6A_16H_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
P. falciparum parasites (in vitro)_Clone 6A (3D7)_16H
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture type: In vitro culture
culture stage: asexual blood stage
clone id (origin): clone 6A (3D7 origin)
clone phenotype: drug-resistant mutant
sampling time point: 16 hr
|
| 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 type: In vitro culture
culture stage: asexual blood stage
strain: laboratory strain 3D7
sample type: mix of several RNA samples collected across the 48-hour 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 |
Microarray hybridizations were carried out using the MAUI hybridization system 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. 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 |
Microarray scanning using Axon 4000B scanner and GenePix Pro v6.0 software (Axon Instruments, USA) was done 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.
|
| Description |
clone 6A TP2 rep1
|
| Data processing |
Data processing 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. In short, background subtracted log2 data was lowess normalized and subsequently filtered for quality control using Acuity 4.0 (Axon Instruments). Only spots with flag>0 and >95% of pixels with median intensity greater than the local background plus 2 times the standard deviation of the background for either dye channel were accepted.
|
| |
|
| Submission date |
Feb 06, 2013 |
| Last update date |
Feb 07, 2013 |
| Contact name |
Sachel Mok |
| E-mail(s) |
moks0007@ntu.edu.sg, sm4223@cumc.columbia.edu
|
| Organization name |
Nanyang Technological University
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11248 |
| Series (2) |
| GSE44127 |
Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum [expression] |
| GSE44129 |
Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum. |
|
