|
| Status |
Public on Jan 07, 2015 |
| Title |
3D7/PfBDP1 OE 4-14hpi |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
3D7/PfBDP1 OE
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
line: 3D7/PfBDP1 OE
genotype/variation: over-expressing PfBDP1-3xHA (3D7/PfBDP1 OE)
culture conditions: 5μg/ml BSD-S-HCl
time point: 4-14 hours post-invasion
life cycle stage: intra-erythrocytic parasites
tissue: whole organism
|
| Treatment protocol |
Pre-synchronized parasite cultures were synchronized twice 14 hours apart to achieve a ten hour growth window. Four consecutive samples were harvested for both 3D7/PfBDP1 OE and 3D7/cam during the intra-erythrocytic cell cycle at 4-14, 24-24, 24-34 and 34-44 hours post-invasion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Ribozol (Amresco) following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Labeling was carried out as described in [PMID: 12929205]
|
| |
|
| Channel 2 |
| Source name |
reference pool RNA
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
sample type: cDNA reference pool consisting of time points 2, 3, 4, 5, 6
tissue: whole organism
|
| Treatment protocol |
Pre-synchronized parasite cultures were synchronized twice 14 hours apart to achieve a ten hour growth window. Four consecutive samples were harvested for both 3D7/PfBDP1 OE and 3D7/cam during the intra-erythrocytic cell cycle at 4-14, 24-24, 24-34 and 34-44 hours post-invasion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Ribozol (Amresco) following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Labeling was carried out as described in [PMID: 12929205]
|
| |
|
| |
| Hybridization protocol |
Microarray hybridizations were carried out as described in [PMID:12929205]. 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 |
Microarrays were scanned as described in PMID: 12929205. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).
|
| Description |
3D7/PfBDP1 OE TP1
|
| Data processing |
Lowess normalisation was applied to all arrays as implemented in the Acuity 4.0 software (Molecular Devices). The microarray data were then filtered to include only spots with at least 95% of pixels having signal intensity greater than two standard deviations above background for both Cy3 and Cy5 fluorescence intensity.
|
| |
|
| Submission date |
Jan 06, 2015 |
| Last update date |
Jan 07, 2015 |
| Contact name |
Michaela Petter |
| E-mail(s) |
mpetter@unimelb.edu.au
|
| Organization name |
University of Melbourne
|
| Department |
Peter Doherty Institute
|
| Street address |
792 Elizabeth Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11248 |
| Series (2) |
| GSE64690 |
Whole genome expression profiling across the life cycle of PfBDP1 overexpressing P. falciparum malaria parasites |
| GSE64691 |
A Novel Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression |
|
