Spatial transcriptomics of mouse spleens during steady state and malaria infection. [d0_d7_slideseqV2]

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 spatial transcriptomics to characterise the microarchitecture of mouse spleen before and during malaria infection, and mapping the spatial and molecular requirements of Tfh/Th1 differentiation. Overall design: Mice were infected with Plasmodium chabaudi chabaudi AS (PcAS) parasitised RBCs (pRBCs) or a saline control. At Day 7, whole spleens were recovered and fresh frozen to generate Slide-seqV2 datasets.