Extended Data Fig. 5: Xenium spatial transcriptomic analysis.
From: Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD
a, Total and unique transcripts per cell for scXenium (top) and per nucleus for snXenium (bottom). b, Cell type spatial co-localization within the tissue section. c, CON and PTSD slides showing nuclei annotated by seven canonical cell types (top) and corresponding H&E images (bottom). Scale bar=1 mm. d, Correlation of MAST log2FC values between snXenium and snRNA for overlapping DEGs across all cell types (r = 0.62). e, Correlation of MAST log2FC values between scXenium and snRNA for overlapping DEGs across all cell types (r = 0.61). f, IN PTSD vs CON volcano plot of snXenium MAST results. DEGs that are labeled and outlined in black overlap with snRNA-seq MAST DEGs. g, CXCL14 log-normalized counts comparing CON and PTSD across cell types. h, CON slide showing individual CXCL14 transcripts in dark green and nuclei with their corresponding cell type colors in a lighter shade (IN = light green). Scale bar=1 mm. CON inset zooms 4X to show individual IN expression. i, PTSD slide showing individual CXCL14 transcripts in dark green and nuclei with their corresponding cell type colors in a lighter shade (IN = light green). Scale bar=1 mm. PTSD inset zooms 4X to show individual IN expression).
