|
| Status |
Public on Feb 08, 2014 |
| Title |
P. falciparum K1 untreated |
| Sample type |
RNA |
| |
|
| Source name |
Parasite trophozoites without treatment incubated for 72 hours
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: K1
treatment: control
|
| Treatment protocol |
P. falciparum was exposed to HDTAB at IC50 value (2 µM) for 72 hours
|
| Growth protocol |
Continuous cultivation of malaria parasite, P. falciparum in vitro was maintained according to the candle jar method of Trager and Jensen (1976) in complete culture medium containing RPMI 1640 (Gibco, USA), 0.2% sodium bicarbonate, 25 mM HEPES, 40 µg/L gentamicin and 10% human serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
the RNA was extracted using Trizol reagent (Invitrogen, USA) followed by purification using Purelink Micro to Midi kit (Invitrogen, USA) and DNase treatment to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
RNA was spiked with eukaryotic poly-A RNA as positive labelling control and was then converted to cDNA using GeneChip® Expression 3’-Amplification Reagent One-Cycle cDNA synthesis kit (Affymetrix, USA). cDNA was purified using the GeneChip sample cleanup kit and then converted to cRNA and biotinylated by incubating with the IVT reaction master mix (1X IVT labelling buffer, IVT labelling NTP mix and IVT labelling enzyme mix) (GeneChip® Expression 3’-Ampification Reagent for IVT labelling kit; Affymetrix). at 37 oC for 16 hours.
|
| |
|
| Hybridization protocol |
Biotinylated cRNA was purified using GeneChip® Sample Cleanup Module kit and 20 µg were fragmented by incubating with fragmenting buffer at 94 oC for 35 min, then mixed with hybridization cocktail (50 pM control oligonucleotide B2, 1X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 1X hybridization mix and 10% DMSO) prior to hybridization onto GeneChip® Plasmodium/Anopheles Genome Array (Affymetrix).
|
| Scan protocol |
The hybridized gene chip was scanned by Affymetric GeneChip Scanner 3000 equipped with GeneChip® Operating Software (GCOS) and GeneChip Fluidics Station 450
|
| Description |
Gene expression data after parasite incubation for 72 hours
|
| Data processing |
The DNA microarray data were analysed using Affymetrix expression console software
|
| |
|
| Submission date |
Feb 07, 2014 |
| Last update date |
Feb 08, 2014 |
| Contact name |
Mohd Ridzuan Mohd Abd Razak |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Medical Research
|
| Street address |
Jalan Pahang
|
| City |
Kuala Lumpur |
| ZIP/Postal code |
50588 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL1321 |
| Series (1) |
| GSE54775 |
Effect of choline kinase inhibitor hexadecyltrimethylammonium bromide on Plasmodium falciparum gene expression |
|
