Data for spatial transcriptomic profiling of murine aortic root plaques from isotype IgG- and anti-PD1-treated Apoe-/- IfngYFP/YFP mice using the 10X Visium platform

This experiment investigates the effects of PD1 immune checkpoint blockade on aortic plaque gene expression in a murine model of atherosclerosis. Eight-week-old female Apoe-/- IfngYFP/YFP mice were fed a high-cholesterol diet for 16 weeks and treated with either isotype IgG (clone 2A3) or anti-PD1 antibody (clone RMP1-14) during the final three weeks (7 doses, biweekly). Formalin-fixed paraffin-embedded (FFPE) heart cross-sections (6 μm) containing the aortic sinus were processed with the 10X Genomics Visium Spatial Gene Expression platform. Count matrices were generated with the Space Ranger pipeline, and data from individual samples were aggregated using the spaceranger aggr function for joint analysis and image alignment. Regions of interest (subvalvular plaques) were subsequently defined in Loupe Browser. The dataset provides spatially resolved transcriptomic profiles of murine aortic plaques under control and PD1 blockade conditions.