SRA

The malaria parasite has a complex lifecycle, including several events of differentiation and stage progression, while actively evading immunity in both its mosquito and human hosts. Important parasite gene expression and regulation during these events remain hidden in rare populations of cells. Here, we combine a capillary-based platform for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single infected red blood cells (sc.iRBCs) during the intra- erythrocyte developmental cycle (IDC). Unbiased analyses of single-cell data grouped the cells into eight transcriptional states during IDC. Interestingly, we uncovered a gene signature from the single iRBC analyses that can successfully discriminate between developing asexual and sexual stage parasites at cellular resolution, and we verify five, previously undefined, gametocyte stage specific genes. Moreover, we show the capacity of detecting expressed genes from the variable gene families in single parasites, despite the sparse nature of data. In total, the single parasite transcriptomics holds promise for molecular dissection of rare parasite phenotypes throughout the malaria lifecycle. Overall design: We combined fully automated CellSorter cell capture system for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single P. falciparum-infected red blood cells (sc.iRBCs) during the intra-erythrocyte developmental cycle (IDC). As a control, we generated 28 RNA-seq libraries from populations (population.iRBCs) containing approximately 5,000 iRBCs at each time point. Please note that only 165 sc.iRBCs libraries which are of moderate to high quality (indicated in the ''library quality'' sample characteristics) were used for the further processing (i.e. 15 samples of low quality have been excluded).