scRNA-seq mouse splenocytes prior to and during blood-stage malaria infection.

Blood-stage malaria infection induces differentiation of several effector CD4 + T subsets including Tfh and Th1 cells. The cues and microarchitectural niches required in secondary lymphoid organs for their formation were previously uncharacterised. Here we used scRNA-seq to profile splenocyte transcriptomes at steady state or upon malaria infection as a reference dataset for deconvolution of spatial transcriptomic data. Overall design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS)-parasitised Red Blood Cells (pRBCs) or a saline control. Splenocytes were recovered at Day 7 post-infection to undergo processing and generate scRNA-seq dataset.