|
| Status |
Public on Jan 07, 2015 |
| Title |
PfBDP1DD OFF Shld1 28+/-4hpi_Bio 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
PfBDP1DD OFF Shld1 28+/-4hpi
|
| Organism |
Plasmodium falciparum 3D7 |
| Characteristics |
transgenic line: PfBDP1-HA-DD
genotype/variation: expressing an endogeneous PfBDP1-HA-DD fusion protein
tissue: whole organsim
transgenic line: PfBDP1-HA-DD
genotype/variation: expressing an endogeneous PfBDP1-HA-DD fusion protein
|
| Treatment protocol |
PfBDP1DD parasites grown in the presence of 2.5 nM WR99210/500 nM Shld1 and synchronized by MACS and sorbitol treatment to an 8-hour growth window were split into two cultures at 30 hours post invasion (hpi) and Shld1 removed from one batch. This is the sample grown in the absence of Shld1.
|
| Growth protocol |
Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life Technologies) 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 |
tissue: whole organsim
sample type: reference pool
|
| Treatment protocol |
RNA from highly synchronized cells was extracted at 6 time points across the IDC at 8 h intervals. Equal amount of RNA from each time point was mixed to prepare the cDNA which was used as a reference pool.
|
| Growth protocol |
Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life Technologies) 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 |
BDP1DD_OFF_TP4_2
|
| 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) |
| GSE64688 |
Whole genome expression profiling across the asexual life cycle in PfBDP1 knockdown malaria parasites |
| GSE64691 |
A Novel Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression |
|
