|
| Status |
Public on Feb 18, 2020 |
| Title |
ACT |
| Sample type |
RNA |
| |
|
| Source name |
Red blood cell
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
tissue: Red blood cell
genotype: wild type (Self-control)
|
| Treatment protocol |
Shiled1 (Clontech, soluble in ethanol, 0.5mM) was added into the culture medium (final concentration: 0.5μM), to induce the degradation of PfSWIB.
|
| Growth protocol |
The P.falciparum lines 3D7, PfSWIB and PfSWIB∆ were first thawed and established for continuous cultivation: thawed isolates were cultured in the RPMI 1640 medium (Invitrogen) containing 25 mM Hepes, 2 mM L-glutamine, 0.1 mM hypoxanthine (Sigma), 20 mg/ml gentamicin (Sigma), 0.5% Albumax II and 2% human serum (type AB+). Cultures were grown in media with type O+ erythrocytes at a 3% hematocrit under 2% O2, 5.5% CO2, 92.5% N2 at 37℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.
|
| |
|
| Hybridization protocol |
DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).
|
| Scan protocol |
Scanned on an Agilent G2565CA scanner.
|
| Description |
Gene expression of wild type (Self-control)
|
| Data processing |
Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.
|
| |
|
| Submission date |
Dec 03, 2019 |
| Last update date |
Feb 18, 2020 |
| Contact name |
Yilong Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Second Military Medical University, Shanghai, China.
|
| Department |
Department of Tropical diseases,
|
| Street address |
No.800 Xiangying road, Yangpu Dirtrict, Shanghai, China.
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL27859 |
| Series (2) |
| GSE141404 |
Screening of differentially expressed genes in three Plasmodium falciparum parasite lines [expression] |
| GSE141959 |
Screening of differentially expressed genes in three Plasmodium falciparum parasite lines |
|
