|
| Status |
Public on Jun 30, 2011 |
| Title |
P. falciparum-thiostrepton-treated-2 |
| Sample type |
RNA |
| |
|
| Source name |
P. falciparum, treated
|
| Organism |
Plasmodium falciparum |
| Characteristics |
treatment: Thiostrepton
|
| Treatment protocol |
Triplicate 15 ml cultures containing synchronous, ring stage parasites at 5 % parasitaemia were treated with 2 uM thiostrepton in DMSO (or 1/2000 vol. DMSO for controls) for 24 hours.
|
| Growth protocol |
Blood stage P. falciparum 3D7 was maintained in continuous culture in vitro at 37 ºC using the candle-jar method. Cultures were maintained in citrated human blood at 2 % hematocrit with complete culture media (RPMI 1640 + L-Glutamine (Gibco) with 5 % w/v AlbuMAX I (Invitrogen), 50 μg.ml-1 hypoxanthine, 25 mM HEPES (Gibco) and 25 μg.ml-1 gentamycin (Sigma), pH of 7.6). Parasitaemia was assessed by thin blood smears stained with Giemsa (Sigma). Percentage infection of red blood cells was determined by cell counts under an oil immersion light microscope. Synchronous parasites were obtained by the Stockholm sorbitol method on two consecutive life cycles
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol (Invitrogen) as described (Kyes, 2004). RNA concentration and purity were determined using a NanoDrop (Thermo) and RNA integrity was tested using an Agilent Bioanalyzer (Cambridge Genomic Services, Department of Pathology)
|
| Label |
Biotin
|
| Label protocol |
Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
|
| |
|
| Hybridization protocol |
Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
|
| Scan protocol |
Microarray cRNA synthesis, hybridisation and plate-reading were conducted by Geneservice (Nottingham, UK).
|
| Description |
Gene expression data from LD70 thiostrepton-treated Plasmodium falciparum
|
| Data processing |
Raw CEL files were imported into Bioconductor (Gentleman et al., 2004) for data analysis. Microarrays were analysed for RNA degradation prior to normalisation. Non-Plasmodium probesets were removed using the altcdfenvs package (Gautier et al., 2004) and microarray data were normalised using GCRMA (Wu et al., 2004). Differential gene expression was analysed using Linear Models for Microarray Analysis (LIMMA) (Smyth, 2004).
|
| |
|
| Submission date |
Apr 19, 2011 |
| Last update date |
Jun 30, 2011 |
| Contact name |
Sarah Tarr |
| E-mail(s) |
[email protected]
|
| Organization name |
UCL
|
| Department |
ISMB
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1321 |
| Series (1) |
| GSE28701 |
Transcript-level responses of Plasmodium falciparum to thiostrepton |
|
