Fig. 2

Spatiotemporal differential gene expression after striatal whole-blood injection. A UMAP plot colored by the unsupervised clustering of the merged spatial transcriptome dataset, including all features from n = 6 mice (no striatal injection [control], different time points after striatal whole-blood injection [2, 12, 24, 48, 96 h]). B Gene set scores for specific anatomical compartments projected on the UMAP plot. TH thalamus, CTX cortex, CP choroid plexus, STR striatum, PAL pallidum, HY hypothalamus, MB midbrain, P Pons. C Mean anatomical gene set expression score (dot color) and fraction of positive features (dot size) of each identified cluster. D Spatial projection of the identified clusters on the control sample (top) and corresponding H&E histology (bottom). E Top five differentially expressed genes (control as baseline) in the CP cluster stratified by time point after injection. F Top five differentially expressed genes (control as baseline) in the STR stratified by time point after injection