|
| Status |
Public on Aug 31, 2021 |
| Title |
PfNot1.1 knockout, TP1, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
P. falciparum T996 RNA, PfNot1.1 knockout
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture, stage, strain, harvest timepoint, estimated developmental age: In vitro culture, asexual blood stage, laboratory strain T996, TP1, 4 hpi
|
| Treatment protocol |
Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction.
|
| Growth protocol |
P. falciparum parasites were cultured in RPMI-HEPES medium , supplemented with 0.25% Albumax , 0.2% sodium bicarbonate, 100 µM hypoxanthine and 10 µg/ml Gentamycin with 2% hematocrit.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| Label |
Cy5
|
| Label protocol |
Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| |
|
| Channel 2 |
| Source name |
P. falciparum 3D7 RNA reference pool
|
| Organism |
Plasmodium falciparum |
| Characteristics |
culture, stage, strain, composition: In vitro culture, asexual blood stage, laboratory strain T996, mixture of equal amounts of RNA harvested every 8 hours over the 48-hour parasite's intraerythrocytic life cycle
|
| Treatment protocol |
Selective drugs were removed from medium two intraerythrocytic life cycles before harvesting parasites for RNA extraction.
|
| Growth protocol |
P. falciparum parasites were cultured in RPMI-HEPES medium , supplemented with 0.25% Albumax , 0.2% sodium bicarbonate, 100 µM hypoxanthine and 10 µg/ml Gentamycin with 2% hematocrit.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| Label |
Cy3
|
| Label protocol |
Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.
|
| |
|
| |
| Hybridization protocol |
Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.
|
| Scan protocol |
Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.
|
| Description |
101045_Cycle1_2017-11-08_KO_TP1_rep2
Transcriptional profiling of the PfNot1.1 knockout line at Timepoint 1 at around 4 hpi, replicate 2
|
| Data processing |
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.
|
| |
|
| Submission date |
Dec 18, 2019 |
| Last update date |
Aug 31, 2021 |
| Contact name |
Ying Liu |
| E-mail(s) |
yliu037@e.ntu.edu.sg
|
| Phone |
84030462
|
| Organization name |
Nanyang Technological University
|
| Department |
School of Biological Sciences
|
| Lab |
Prof. Zbynek Bozdech's lab
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11248 |
| Series (1) |
| GSE142275 |
Transcriptional profilling of Plasmodium falciparum parasites with disrupted PfNot1.1 (PF3D7_1103800) or PfNot1.2 (PF3D7_1417200) |
|
