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.
Project description:Transcription profile of the Plasmodium vivax intraerythrocytic cycle Total RNA in Plasmodium vivax strain at every 6 hour of intraerythrocytic cycle using RNA-seq
Project description:The objective of this study is to characterize the overall transcriptome of P. falciparum NF54 derived from a controlled-human malaria infection (CHMI) study. Healthy, immunologically naïve human volunteers were infected intradermally or intravenously with different dosages of Plasmodium falciparum sporozoites (Sanaria® PfSPZ Challenge). Parasites were isolated from these volunteers and subjected to a range of in vitro culture generation prior to RNA collection.