|
| Status |
Public on Feb 07, 2013 |
| Title |
clone11C_gDNA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
P. falciparum parasites (in vitro), Clone 11C (3D7)
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture type: In vitro culture
culture stage: asexual blood stage
clone id (origin): clone 11C (3D7 origin)
clone phenotype: drug-sensitive wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted using phenol-chloroform and as previously 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.
|
| Label |
Cy5
|
| Label protocol |
Synthesis of aminoallyl-coupled DNA by klenow reaction and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu & J. L. DeRisi, (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5.
|
| |
|
| Channel 2 |
| Source name |
P. falciparum 3D7 genomic DNA
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture type: In vitro culture
culture stage: asexual blood stage
strain: laboratory strain 3D7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted using phenol-chloroform and as previously 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.
|
| Label |
Cy3
|
| Label protocol |
Synthesis of aminoallyl-coupled DNA by klenow reaction and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu & J. L. DeRisi, (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5.
|
| |
|
| |
| 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.
|
| 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 |
GPL11250 |
| Series (2) |
| GSE44128 |
Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum [CGH] |
| GSE44129 |
Structural polymorphism in the promoter of pfmrp2 confers tolerance to mefloquine and chloroquine in Plasmodium falciparum. |
|
