|
| Status |
Public on Jul 15, 2014 |
| Title |
KH003-021-199016 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
P. falciparum field isolate, Rattanakiri Cambodia, KH003-021
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture: in vivo
Stage: blood
patient sample id: KH003-021
geographic origin: Rattanakiri, Cambodia
barcode: 199016
timepoint: prior to artemisinin combination therapy (ACT)
parasite clearance halflife upon artemisinin treatment (h): 3.753h
|
| 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 |
strain/background: 3D7
culture: In vitro
Stage: asexual blood
composition: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle
sample type: reference
|
| 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 |
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.
|
| Description |
KH003-021-199016
Reference sample is laboratory strain 3D7.
|
| 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 |
Jul 05, 2014 |
| Last update date |
Jul 15, 2014 |
| 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 |
GPL18893 |
| Series (2) |
| GSE59097 |
Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates [in vivo] |
| GSE59099 |
Whole genome expression profiling of artemsinin-resistant Plasmodium falciparum field isolates |
|
