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Transcriptomic changes in P. falciparum upon knockdown of PfGCN5

ABSTRACT: Transcriptomic changes in P. falciparum upon knockdown of PfGCN5

PROVIDER: PRJNA1198376 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31751102_1.fastq.gz	Fastqsanger.gz
	SRR31751102_2.fastq.gz	Fastqsanger.gz
	SRR31751104_1.fastq.gz	Fastqsanger.gz
	SRR31751104_2.fastq.gz	Fastqsanger.gz
	SRR31751107_1.fastq.gz	Fastqsanger.gz

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Transcriptomic changes in P. falciparum upon knockdown of PfGCN5

Project description:This study is to analyze the overal transcriptomic alteration after knockdown of PfGCN5 by TetR-DOZI system. The transcriptomic changes of a parasite line (TetR-PfGCN5::GFP) after PfGCN5 knockdown (KD) by withdral of anhydrotetracycline (aTc) compared to its control (TetR-PfGCN5::GFP with aTc) were analyzed during asexual stage development fron ring, to schizont stage by RNAseq. Total RNA were harvested from four stage (ring, early trophozoite, late trophozoite, and schizont) 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. Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2. 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. Differential expression analysis showed that PfGCN5 KD profoundly changed the global transcription pattern. GO enrichment analysis indicated that PfGCN5 was involved in general and parasite-specific gene transcription. Collectively, transcriptomic analysis of PfGCN5 KD shows that PfPfGCN5 plays important role in global gene regulation .

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