|
| Status |
Public on Jan 27, 2021 |
| Title |
Time 0h, Rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
FOS-treated NF54, Time 0, Rep 1
|
| Organism |
Plasmodium falciparum |
| Characteristics |
protocol: Blood-stage NF54 P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 1 uM fosmidomycin
time: 0h
replicate: Rep 1
|
| Treatment protocol |
Sub-lethal dose of fosmidomycin (1 uM) was added to control RPMI medium at 0 h of the experiment, which was determined using blood smears of the parasite cultures (described in the paper).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.
|
| Label |
Cy3
|
| Label protocol |
From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).
|
| |
|
| Hybridization protocol |
The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate.
|
| Scan protocol |
Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.
|
| Description |
Gene expression data
|
| Data processing |
Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.
|
| |
|
| Submission date |
Oct 19, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Shivendra G Tewari |
| E-mail(s) |
stewari@bhsai.org
|
| Phone |
3016191942
|
| Organization name |
Biotechnology HPC Software Applications Institute
|
| Street address |
2405 Whittier Drive, Suite 200
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL27130 |
| Series (1) |
| GSE159516 |
Metabolic survival adaptations of Plasmodium falciparum exposed to sub-lethal doses of fosmidomycin |
|
