|
| Status |
Public on Aug 21, 2019 |
| Title |
T1041.3200IV.42.5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Plasmodium falciparum, CHMI-derived
|
| Organism |
Plasmodium falciparum NF54 |
| Characteristics |
sample type: CHMI-derived
tuchmi id: T1041
culture: In vitro, blood stage
pfspz dose: 3200IV
gpi: t4
|
| Treatment protocol |
NA
|
| Growth protocol |
All P. falciparum isolates were cultivated at 5% haematocrit of O+ erythrocytes. RPMI 1640 medium was completed with 10% Albumax (Gibco), 25mM Hepes Buffer, 2mM L-Glutamine and 0.05mg/ml gentamicin (all PAA Laboratories). Parasites were incubated at 37°C in 90% nitrogen, 5% oxygen and 5% carbon dioxide.
|
| 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 |
Labeling of cDNA was performed 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 |
Plasmodium falciparum, reference
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
sample type: Reference
culture: In vitro, blood stage
composition: Mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle.
|
| Treatment protocol |
NA
|
| Growth protocol |
All P. falciparum isolates were cultivated at 5% haematocrit of O+ erythrocytes. RPMI 1640 medium was completed with 10% Albumax (Gibco), 25mM Hepes Buffer, 2mM L-Glutamine and 0.05mg/ml gentamicin (all PAA Laboratories). Parasites were incubated at 37°C in 90% nitrogen, 5% oxygen and 5% carbon dioxide.
|
| 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 |
Labeling of cDNA was performed 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 |
Hybridization of labeled cDNA was performed 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.
|
| Scan protocol |
Scanning and image acquisition of the hybridized microarray chips was performed using the PowerScannerTM (Tecan) at 10µM resolution under automated photomultiplier (PMT) balancing. Hybridized spots were analysed and preprocessed using GenePix® ProMicroarray Image Analysis Software v6.0 (Axon Instruments).
|
| Description |
in vitro culture derived from CHMI
|
| 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 |
Aug 20, 2019 |
| Last update date |
Aug 21, 2019 |
| Contact name |
Regina Hoo |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Science
|
| Street address |
60, Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18893 |
| Series (1) |
| GSE136076 |
Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies |
|
