Journal: NAR Genomics and Bioinformatics
Article Title: SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics
doi: 10.1093/nargab/lqag039
Figure Lengend Snippet: SpNeigh reveals intermediate cell populations near boundaries in mouse brain Xenium data. ( a ) Spatial plots showing different annotation types. Left: Cells colored by clusters with overlaid boundaries of cluster 2. Middle: Manual cluster-level annotations based on brain anatomy. Right: Reference-based single-cell annotations, with selected subtypes merged. CGE: caudal ganglionic eminence; MGE: medial ganglionic eminence. ( b ) Neighborhood analysis of cluster 2. Top: Boundary and ring regions. Bottom: Cells within boundary and ring regions for region 1, with donut plots showing cluster proportions (labels shown for proportions \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\ge$\end{document} 5%). ( c ) Expression of Slc17a7 and Sox10 in cluster 2 cells inside boundaries and surrounding rings. Slc17a7, a marker of cortical excitatory neurons, shows elevated expression in outer cells near the boundary. Sox10 is broadly expressed in oligodendrocytes and remains consistent across both inner and outer cells in cluster 2. ( d ) Boundary 1 of cluster 2 split into discrete edges. ( e ) Spatial weights relative to edge 2 for cortical cells. Black line indicates edge 2. ( f ) Top spatially varying genes identified by RunSpatialDE using weights from edge 2. ( g ) Expression of Ccn2 and Cplx3 near edge 2. Cells include cortical layer 4/5/6 neurons, L6b neurons, astrocytes, and oligodendrocytes. L6b cells are localized along edge 2.
Article Snippet: Mouse brain tiny Xenium dataset: https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-for-xenium-explorer-demo-1-standard .
Techniques: Single Cell, Expressing, Marker
![SpNeigh reveals intermediate cell populations near boundaries in <t>mouse</t> <t>brain</t> <t>Xenium</t> data. ( a ) Spatial plots showing different annotation types. Left: Cells colored by clusters with overlaid boundaries of cluster 2. Middle: Manual cluster-level annotations based on brain anatomy. Right: Reference-based single-cell annotations, with selected subtypes merged. CGE: caudal ganglionic eminence; MGE: medial ganglionic eminence. ( b ) Neighborhood analysis of cluster 2. Top: Boundary and ring regions. Bottom: Cells within boundary and ring regions for region 1, with donut plots showing cluster proportions (labels shown for proportions \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\ge$\end{document} 5%). ( c ) Expression of Slc17a7 and Sox10 in cluster 2 cells inside boundaries and surrounding rings. Slc17a7, a marker of cortical excitatory neurons, shows elevated expression in outer cells near the boundary. Sox10 is broadly expressed in oligodendrocytes and remains consistent across both inner and outer cells in cluster 2. ( d ) Boundary 1 of cluster 2 split into discrete edges. ( e ) Spatial weights relative to edge 2 for cortical cells. Black line indicates edge 2. ( f ) Top spatially varying genes identified by RunSpatialDE using weights from edge 2. ( g ) Expression of Ccn2 and Cplx3 near edge 2. Cells include cortical layer 4/5/6 neurons, L6b neurons, astrocytes, and oligodendrocytes. L6b cells are localized along edge 2.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_9690/pmc13069690/pmc13069690__lqag039fig2.jpg)