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spatial transcriptomics based cellchat analysis  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc spatial transcriptomics based cellchat analysis
    Spatial Transcriptomics Based Cellchat Analysis, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/spatial+transcriptome+analysis/analysis+based+cellchat+spatial+transcriptomics/pm41833005-143-6-6
    Average 86 stars, based on 1 article reviews
    spatial transcriptomics based cellchat analysis - by Bioz Stars, 2026-10
    86/100 stars

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    Article Title: Recent advances in understanding neuronal diversity and neural circuit complexity across different brain regions using single-cell sequencing
    Article Snippet: Single-cell transcriptome profiling technology (spatial transcriptomics) , Single cell level , MERFISH , Currently up to 500 selected genes , All cell types , Fresh frozen, PFA-fixed frozen tissue, paraffin-embedded tissue.

    Article Title: Senescent cells as a target for anti-aging interventions: From senolytics to immune therapies
    Article Snippet: [ , ] Whereas single-cells technologies are typically devoid of original tissue context, a recent work engaging multi-organ spatial transcriptome sequencing (stRNA-seq, spatial transcriptomics RNA sequencing) provided a panoramic multi-organ characterization of tissue senescence in aged mice and identify the aggregation of immunoglobulin G (IgG) as a marker and inducer of tissue senescence, unveiling a novel molecular target for senescence-targeted interventions.

    RNA Sequencing:

    Article Title: Spatial omics in 3D culture model systems: decoding cellular positioning mechanisms and microenvironmental dynamics
    Article Snippet: 2025 , Smart-seq3D (scRNA + diffusion labeling) , TNBC tumor spheroids (3D culture) , Inferred radial positions of cells in spheroids via dye diffusion and Smart-seq3; identified thousands of spatially variable genes and continuous core–periphery expression gradients, capturing 3D-specific heterogeneity. , [ ] . .. 2024 , HiFi-Slide spatial RNA sequencing , BBB assembloid (PSC-derived brain + vasculature) , Achieved 3D spatial transcriptomics on a PSC-derived brain–blood-vessel assembloid; identified 12 spatial domains and colocalized cell types (e.g. ECs with GABAergic neurons, SMCs with glutamatergic neurons), recapitulating neurovascular arrangement. , [ ] . .. 2023 , MALDI-MSI (metabolomics) , Cortical brain organoid (human iPSC) , Optimized mass spec imaging of organoid sections; detected ~ 260 lipids and mapped their localization. Found lipid species enriched in neurogenic rosettes, suggesting roles in progenitor maintenance vs. differentiation. , [ ] .

    Article Title: Normal Ageing Impacts the Extent and Diversity of Neural Plasticity Induced in the Mouse Brain With Repetitive Transcranial Magnetic Stimulation.
    Article Snippet: .. 3.1 | Spatial Transcriptomics Uncovers Cortical Region and Layer Dependent Neural Plasticity Mechanisms of Subthreshold Theta Burst rTMS in the Aged Brain To determine whether rTMS has a large gross effect on the cortex, we first used whole transcriptome bulk RNA- sequencing from dissected sensorimotor tissue (i.e., motor and somatosensory cortex dissected together) (Figure 1a). ..

    Spatial Transcriptomics:

    Article Title: Spatial omics in 3D culture model systems: decoding cellular positioning mechanisms and microenvironmental dynamics
    Article Snippet: 2025 , Smart-seq3D (scRNA + diffusion labeling) , TNBC tumor spheroids (3D culture) , Inferred radial positions of cells in spheroids via dye diffusion and Smart-seq3; identified thousands of spatially variable genes and continuous core–periphery expression gradients, capturing 3D-specific heterogeneity. , [ ] . .. 2024 , HiFi-Slide spatial RNA sequencing , BBB assembloid (PSC-derived brain + vasculature) , Achieved 3D spatial transcriptomics on a PSC-derived brain–blood-vessel assembloid; identified 12 spatial domains and colocalized cell types (e.g. ECs with GABAergic neurons, SMCs with glutamatergic neurons), recapitulating neurovascular arrangement. , [ ] . .. 2023 , MALDI-MSI (metabolomics) , Cortical brain organoid (human iPSC) , Optimized mass spec imaging of organoid sections; detected ~ 260 lipids and mapped their localization. Found lipid species enriched in neurogenic rosettes, suggesting roles in progenitor maintenance vs. differentiation. , [ ] .

    Article Title: Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.
    Article Snippet: .. Other studies performed SARS-CoV-2 detection by targeting a limited number of genes with RNAScope [37] or viral proteins with immunohistochemistry [38] in sections consecutive to those processed for human whole-transcriptome analysis with Spatial Transcriptomics (10X Genomics Visium platform). ..

    Article Title: Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BWA2 Bioconductor v. 0.7.17 Picard Broad institute v. 2.17.11 GATK Broad institute v.4.2.2.0 Mutect2 Broad institute v4.1.0.0 maftools Bioconductor v.2.12.0 edgeR Bioconductor v.3.40.2 Cell Reports Medicine 5, 101610, June 18, 2024 e2 .. Spatial transcriptomics experiment and analysis GeoMxR Human Whole Transcriptome atlas (GeoMx Hu WTA) was used for the tumors selected for spatial transcriptomic analysis under a special early access program. ..

    Article Title: Reconstructing Coherent Functional Landscape From Multi-Modal Multi-Slice Spatial Transcriptomics by a Variational Spatial Gaussian Process.
    Article Snippet: .. Spatial transcriptomics (ST) technologies enable highthroughput gene expression profiling while preserving spatial context within tissues in situ [ 1–5 ]. ..

    RNAscope:

    Article Title: Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.
    Article Snippet: .. Other studies performed SARS-CoV-2 detection by targeting a limited number of genes with RNAScope [37] or viral proteins with immunohistochemistry [38] in sections consecutive to those processed for human whole-transcriptome analysis with Spatial Transcriptomics (10X Genomics Visium platform). ..

    Immunohistochemistry:

    Article Title: Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.
    Article Snippet: .. Other studies performed SARS-CoV-2 detection by targeting a limited number of genes with RNAScope [37] or viral proteins with immunohistochemistry [38] in sections consecutive to those processed for human whole-transcriptome analysis with Spatial Transcriptomics (10X Genomics Visium platform). ..

    High Throughput Screening Assay:

    Article Title: HIDF: Integrating Tree-Structured scRNA-seq Heterogeneity for Hierarchical Deconvolution of Spatial Transcriptomics.
    Article Snippet: .. Advances in Spatial Transcriptomics (ST) enable highthroughput analysis of gene expression profiles within the spatial context of tissues,[1] providing unprecedented insights into the distribution of cellular heterogeneity within complex structures, such as brain organization,[2,3] tumor microenvironments,[4,5] and immune niches. ..

    Article Title: Reconstructing Coherent Functional Landscape From Multi-Modal Multi-Slice Spatial Transcriptomics by a Variational Spatial Gaussian Process.
    Article Snippet: .. Spatial transcriptomics (ST) technologies enable highthroughput gene expression profiling while preserving spatial context within tissues in situ [ 1–5 ]. ..

    Gene Expression:

    Article Title: HIDF: Integrating Tree-Structured scRNA-seq Heterogeneity for Hierarchical Deconvolution of Spatial Transcriptomics.
    Article Snippet: .. Advances in Spatial Transcriptomics (ST) enable highthroughput analysis of gene expression profiles within the spatial context of tissues,[1] providing unprecedented insights into the distribution of cellular heterogeneity within complex structures, such as brain organization,[2,3] tumor microenvironments,[4,5] and immune niches. ..

    Article Title: Reconstructing Coherent Functional Landscape From Multi-Modal Multi-Slice Spatial Transcriptomics by a Variational Spatial Gaussian Process.
    Article Snippet: .. Spatial transcriptomics (ST) technologies enable highthroughput gene expression profiling while preserving spatial context within tissues in situ [ 1–5 ]. ..

    Preserving:

    Article Title: Reconstructing Coherent Functional Landscape From Multi-Modal Multi-Slice Spatial Transcriptomics by a Variational Spatial Gaussian Process.
    Article Snippet: .. Spatial transcriptomics (ST) technologies enable highthroughput gene expression profiling while preserving spatial context within tissues in situ [ 1–5 ]. ..

    In Situ:

    Article Title: Reconstructing Coherent Functional Landscape From Multi-Modal Multi-Slice Spatial Transcriptomics by a Variational Spatial Gaussian Process.
    Article Snippet: .. Spatial transcriptomics (ST) technologies enable highthroughput gene expression profiling while preserving spatial context within tissues in situ [ 1–5 ]. ..



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    Spatial Transcriptomics Inc spatial transcriptomics data analysis
    a Schematic diagram of the spatial <t>transcriptome</t> 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.
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    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.

    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