scRNA-seq + TCR-seq of mouse polyclonal CD4+ T cells 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 CD4+ T cell transcriptomes upon malaria infection as a reference dataset for deconvolution of spatial transcriptomic data. Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS)-parasitised Red Blood Cells (pRBCs). CD4+ T cells were recovered at Day 7 post-infection to undergo processing and generate scRNA-seq dataset.