Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)

CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. Here, we applied spatial transcriptomics to explore cellular localization and potential interaction between key immune cell subsets during chronic LCMV Clone 13 infection. Spleens from Control or CD4+ T cell-depleted mice on Day 7 and Day 21 post-LCMV Cl13 infection (2 mice per condition total, conducted in two separate rounds of experiments) and were frozen fresh, stored, and processed as instructed by the Visium kit (10x Genomics). 10 μm sections were generated from frozen spleens and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Spleen tissue on Visium slides was permeabilized for 18 minutes to extract mRNA and downstream library preparation and sequencing were conducted according to manufacturer’s protocol.