|
| Status |
Public on Mar 01, 2012 |
| Title |
P. falciparum NF54-3 |
| Sample type |
RNA |
| |
|
| Source name |
Asynchronous culture of P. falciparum NF54 erythrocytic forms in O+ RBCs
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: NP54
culture: Asynchronous: 80% Rings + trophozoites
|
| Treatment protocol |
Paired parasite cultures were grown till 8-10% parasitemia and then processed for microarray analysis.
|
| Growth protocol |
P. falciparum NF54 was cultured in O+ RBCs under 3% O2, 4% CO2, 93% N2 at 37 °C. P. falciparumHOX was cultured in O+ RBCsunder 5% CO2/95% air (~19% O2) at 37 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Homogenization and lysis of cells with Lysing Matrix D (MP Biomedicals) in Trizol (Invitrogen) with FastPrep120 (MP Biomedicals) instrument. Purification with Qiagen RNeasy Mini kit. All performed according to the manufacturers' instructions.
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA was processed according to Affymetrix 3' IVT Express Manual.
|
| |
|
| Hybridization protocol |
Fragmented, biotinylated cRNA was hybridized to Plasmodium/Anoptheles GeneChips for 16hours at 45°C and 60rpm. Affymetrix recommended signal amplification protocol for washing/staining of Eukaryotic targets was performed in a FS450 automated fluidics station.
|
| Scan protocol |
GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.
|
| Description |
NF54 3_control
Gene expression data from P. falciparum NF54 grown in 3% O2, 4% CO2, 93% N2
|
| Data processing |
The data were analyzed with Partek Genomics Suite software, version 6.5. GC-RMA algorithm defaults were used background correction (GC-RMA), normalization (Quantile) and summarization (median polish) of probesets.
|
| |
|
| Submission date |
Nov 19, 2011 |
| Last update date |
Mar 01, 2012 |
| Contact name |
Rahul Prakash Bakshi |
| E-mail(s) |
rbakshi@jhmi.edu
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Medicine/Clinical Pharmacology
|
| Lab |
Shapiro
|
| Street address |
303 Hunterian 725 N Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL1321 |
| Series (1) |
| GSE33826 |
Gene expression in Plasmodium falciparum NF54 and P. falciparum HOX |
|
