xenium in situ spatial transcriptomic analysis  (10X Genomics)

Journal: bioRxiv

Article Title: CXCL10 drives female-specific tau pathology progression and defines sex-dependent vulnerability in tauopathy model mice

doi: 10.64898/2026.04.19.719088

Figure Lengend Snippet: a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

Article Snippet: FFPE brain sections were analyzed using Xenium spatial transcriptome analysis (10x Genomics).

Techniques: Formalin-fixed Paraffin-Embedded, Olfactory, Gene Expression

Journal: Biomarker Research

Article Title: Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy

doi: 10.1186/s40364-024-00636-3

Figure Lengend Snippet: Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

Article Snippet: Fig. 6 Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections.

Techniques: Control, Expressing, Marker