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Plasmodium knowlesi strain H

ABSTRACT: RNA-seq of Plasmodium knowlesi

PROVIDER: PRJDB12907 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR343853.fastq.gz	Fastqsanger.gz
	DRR343854.fastq.gz	Fastqsanger.gz
	DRR343855.fastq.gz	Fastqsanger.gz
	DRR343856.fastq.gz	Fastqsanger.gz
	DRR343857.fastq.gz	Fastqsanger.gz

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Global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites

Project description:The purpose of this research is to identify and evaluate the global gene expression of the rodent malaria parasites Plasmodium yoelii, Plasmodium berghei and Plasmodium chabaudi blood-stage parasites and specifically compare the blood stage gene expression profiles of samples derived from previous studies on Plasmodium falciparum, Plasmodium vivax and Plasmodium knowlesi

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Plasmodium knowlesi strain H

Project description:Plasmodium knowlesi

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Novel single-cell preservation and RNA sequencing technology unlocks field studies for Plasmodium natural infections

Project description:Single-cell RNA sequencing (scRNA-seq) is a powerful technology that can be used to unravel cellular heterogeneity when applied to unicellular eukaryotes, including Plasmodium parasites. scRNA-seq is particularly useful to study complex infections like malaria, with mixed life stages or clones, yet until now it has been primarily limited to in vitro and animal malaria models due to challenges associated with working with malaria natural infections in endemic settings. We validated a novel single-cell RNA sequencing technology for use with Plasmodium parasites by combining optimized sample preparation methods with RNA preservation integrated in a sample capture device, which allows for the separation of the sample collection and library preparation and sequencing. We recovered 22,345 P. knowlesi single-cell transcriptomes from 6 samples, the most extensive P. knowlesi dataset to date. Regardless of preparation methods used, all samples resulted in reproducible circular UMAP projections with consistent cluster localization and high gene expression correlation, which were confirmed by biomarker expression and annotating life stages using the Malaria Cell Atlas P. knowlesi reference dataset. Some variation in life stage recovery was observed, especially for the ring stage. This could be attributed to the inherent differences between sample preparation methods, or as a result of gene and transcript filtering thresholds which should be further investigated and optimized based on what is known about parasite biology. In conclusion, by combining parasite enrichment with a novel scRNA-seq and preservation technology, scRNA-seq can be expanded to field settings, even when limited resources are available.

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Transcriptional signature of CD4hiCD38hi T cells from patients with Plasmodium falciparum or Plasmodium knowlesi malaria

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Proteomics analysis of P. knowlesi mutants

Project description:Mass spectrometry-based identification of mutated and wild-type Plasmodium falciparum lysyl tRNA synthetase (PfKRS) in Plasmodium knowlesi.

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Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures

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Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures

Project description:The purpose of this reasearch is to identify and evaluate the global gene expression of Plasmodium knowlesi blood-stage parasites and specifically compare the gene expression profiles of samples derived from ex vivo versus long-term in vitro cultures. For ex vivo samples, a rhesus monkey was infected with P. knowlesi to obtain ring iRBCs to establish a short-term culture to immediately collect ex vivo derived time points every 4 hours in the course of the parasite’s 24-hour life cycle. For in vivo samples, they were generated from the same clone in the ex vivo culture adapted to long-term in vitro culture and were collected every 4 hours in the course of the parasite's 24-hour life cycle. Two replicate experiments(Aa and Ha) were developed from in vitro cultures. Samples labeled with Cy5 were hybridized against a reference RNA pool labeled with Cy3, consisting of equal amounts of P. knowlesi RNA from each time point.

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Project description:Plasmodium knowlesi Raw sequence reads

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