Extended Data Fig. 4: Related to Fig. 3. Immune response to LCMV profiled by whole-transcriptome spatial sequencing of the mouse small intestine.
From: Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted
a, VisiumHD results on mouse small intestine roll 8 days after LCMV infection colored by graph-based clustering. b, VisiumHD spots colored by imputed crypt-villus axis values. c, Ratios of overlapping gene expression at the top vs. bottom in epithelial cells from day 8 pi Xenium and VisiumHD dataset. r: Pearson correlation coefficient. d, Convolved gene expression of cytokines along the imputed crypt-villus axis in the VisiumHD dataset. Red labels indicate genes that were included in the Xenium gene panel. e, Transcript reassigning based on H&E nuclei segmentation to achieve single-nuclei level gene expression data (left) and example (right). Reg3b is plotted to showcase the single-nuclei level data. f, Incoming signals across CD8αβ regional subtypes in the VisiumHD dataset.
