Fig. 2: Spatial transcriptomic analysis of the PTSD PFC.
From: Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD
a, Sample description and UMAP of snXenium (n = 523,314 nuclei) across seven cell types (top) and proportion of cell types across conditions (bottom). b, Expression of canonical markers for cell-type annotation (diagonal). The circle radius represents the fraction of cells, and the shade represents mean log-normalized expression. c, PTSD snXenium DEG counts in both directions using MAST. d, Overlap between PTSD snRNA-seq and snXenium MAST DEGs (lighter shade denotes snRNA-seq, and darker shade indicates snXenium). e, Volcano plot showing PTSD versus CON MAST DEGs in END from snXenium. Genes labelled and outlined in black overlap with snRNA-seq END MAST results. Horizontal dashed line indicates FDR < 0.01 and vertical dashed line indicates absolute fold change >1.1. f, Mean FKBP5 log-normalized counts comparing n = 10 CON versus n = 4 PTSD samples by cell type. g, CON slide with FKBP5 transcripts indicated in dark purple and each nucleus in its corresponding cell-type colour (END in light purple). The zoomed-in image in the inset shows a local blood vessel with high FKBP5 expression. One experiment was conducted. h, PTSD slide with FKBP5 transcripts indicated in dark purple and each nucleus in its corresponding cell-type colour (END in light purple). One experiment was conducted.
