scRNA-seq of rodent malaria parasites (P. berghei) and their host cells in spleen, bone marrow and blood. scRNA-seq of rodent malaria parasites (P. berghei) and their host cells in spleen, bone marrow and blood

The malaria parasite Plasmodium replicates and differentiates in red blood cells of its host. The erythropoietic niches (spleen and bone marrow) are important but poorly understood reservoirs of asexual replication and sexual development. We aimed to understand how the parasite adapts to its host organ and a host cell level. For this, we performed single-cell RNA-seq (scRNA-seq) analysis on host and parasite cells derived from spleen, blood and bone marrow. Organs were harvested from two infected and one uninfected mice and parasite cells were enriched to about 50% by flow sorting (infected samples only). To identify host cells by surface expression (CITE-seq), cells were stained with barcoded antibodies targeting CD44 and CD71. Droplet-based scRNA-seq of these samples was performed using 10X genomics technology and cDNA was sequenced on Illumina.

疟原虫（Plasmodium）会在宿主的红细胞内完成增殖与分化。造血微环境（脾脏与骨髓）是疟原虫进行无性增殖与有性发育的重要定植场所，但其相关机制目前仍缺乏深入认知。本研究旨在解析疟原虫如何适应宿主器官及宿主细胞层面的微环境。为此，我们对取自脾脏、血液与骨髓的宿主细胞及疟原虫细胞开展了单细胞RNA测序（single-cell RNA-seq, scRNA-seq）分析。实验样本取自2只感染小鼠与1只未感染小鼠，仅感染组样本通过流式分选将疟原虫细胞富集至约50%的占比。为通过表面标志物表达鉴定宿主细胞（采用CITE-seq技术），我们使用靶向CD44与CD71的条形码标记抗体对细胞进行染色。本研究采用10X Genomics技术对上述样本开展基于微滴的scRNA-seq，并在Illumina平台上完成cDNA测序。