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| Status |
Public on Feb 08, 2023 |
| Title |
Transcriptome of ring-stage parasites responses to stress conditions upon knockdown of PfGCN5 |
| Organism |
Plasmodium falciparum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: this study is to analyze the change of overal transcriptome after three stress conditions in ring-stage Plasmodium falciparum before and after knockdown of PfGCN5 by TetR-DOZI system.
Methods: In this study, the transcriptomes of a parasite line (TetR-PfGCN5::GFP) for knockdown (KD) of PfGCN5 by withdral of anhydrotetracycline (aTc) comparing to its control (TetR-PfGCN5::GFP with aTc) under three stress conditions [HS: heat shock, low-glucose starvation: L-Glu, and low dose of dihydroartemisinin (DHA) treatment] were analyzed at ring stage by RNAseq. Total RNA were harvested from the eary ring stages after 6 h of stress conditions using the Quick-RNA MiniPrep kit (Zymo Research). RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2.
Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified over 5 thousands transcripts with high mapping rate at the range between 80% and 95. PfGCN5 KD profoundly changed the global transcription pattern upon stress conditions, indicating PfGCN5 is involved in stress responses.
Conclusions: Collectively, transcriptomic analysis of PfGCN5-dependent stress responses shows PfPfGCN5 plays important role in gene regulation of stress responses.
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| Overall design |
mRNA profiles of TetR-PfGCN5::GFP with aTc, TetR-PfGCN5::GFP without aTc under three stress conditions (HS, L-Glu and DHA) were generated by deep sequencing, in two or three replicates
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| Contributor(s) |
Miao J, Cui L |
| Citation(s) |
36711954, 37702516 |
| |
| Submission date |
Dec 16, 2022 |
| Last update date |
Oct 31, 2023 |
| Contact name |
JUN MIAO |
| E-mail(s) |
jmiao1@usf.edu
|
| Phone |
8139747374
|
| Organization name |
University of South Florida
|
| Department |
Internal Medicine
|
| Lab |
Jun Miao and Liwang Cui
|
| Street address |
3720 Spectrum Boulevard, MDC84
|
| City |
Tampa |
| State/province |
Florida |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL26920 |
NextSeq 550 (Plasmodium falciparum) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA913193 |
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