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10x xenium spatial transcriptomics analysis  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc 10x xenium spatial transcriptomics analysis
    10x Xenium Spatial Transcriptomics Analysis, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/xenium+spatial+transcriptome+analysis/10x+spatial+transcriptomics/pm40593805-158-11-0
    Average 90 stars, based on 1 article reviews
    10x xenium spatial transcriptomics analysis - by Bioz Stars, 2026-09
    90/100 stars

    Images

    Related Articles

    Imaging:

    Article Title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC
    Article Snippet: .. For each patient core (in the BSW Discovery cohort, 3 mm diameter) analyzed using imaging mass cytometry, 10X spatial transcriptomics or Nanostring Geo Mx Digital Spatial Profiling (DSP), ROIs were selected based on two parameters- tumor location (center vs periphery) and amount of immune infiltration observed in the H&E section (immune rich vs immune poor). ..

    Mass Cytometry:

    Article Title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC
    Article Snippet: .. For each patient core (in the BSW Discovery cohort, 3 mm diameter) analyzed using imaging mass cytometry, 10X spatial transcriptomics or Nanostring Geo Mx Digital Spatial Profiling (DSP), ROIs were selected based on two parameters- tumor location (center vs periphery) and amount of immune infiltration observed in the H&E section (immune rich vs immune poor). ..

    Spatial Transcriptomics:

    Article Title: Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC
    Article Snippet: .. For each patient core (in the BSW Discovery cohort, 3 mm diameter) analyzed using imaging mass cytometry, 10X spatial transcriptomics or Nanostring Geo Mx Digital Spatial Profiling (DSP), ROIs were selected based on two parameters- tumor location (center vs periphery) and amount of immune infiltration observed in the H&E section (immune rich vs immune poor). ..

    Article Title: Uncovering the Regional and Cell Specific Bioactivity of Injectable Extracellular Matrix Biomaterials in Myocardial Infarction through Spatial and Single Nucleus Transcriptomics
    Article Snippet: Half of the animal hearts per each model group were used were cut into 6 slices using a stainless-steel rat heart slicer matrix (Zivic Instruments) with 1.0 mm coronal spacing. .. Odd slices were frozen in TissueTek OCT TM and sectioned into 10 μm thick slices and placed onto a 10X Visium Spatial Transcriptomics Slide or a regular histology slide. ..

    Article Title: Coevolution of neoplastic and non-neoplastic reactive astrocyte states converges on mesenchymal-like and injury-response programs during murine glioblastoma progression and post-radiotherapy recurrence
    Article Snippet: .. Tumor samples intended for 10x Spatial Transcriptomics were immediately snap-frozen in isopentane on dry ice, while the remaining tissues were placed in pre-chilled PBS on ice. .. Whole brain from euthanized animals embedded in Optimal Cutting Temperature Compound (OCT) (Thermo Fisher Scientific) were snap-frozen in ice-cold isopentane.

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. ( A ) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. ( B ) Heatmap of top differentially expressed genes for each spatial domain. ..

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice.
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. (A) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. (B) Heatmap of top differentially expressed genes for each spatial domain. ..

    Article Title: Spatial and single cell mapping of castleman disease reveals key stromal cell types and cytokine pathways.
    Article Snippet: .. Spatial transcriptomics analysis of a validation cohort of CD We performed 10x Xenium spatial transcriptomics analysis in a validation cohort of 13 CD cases and controls. ..

    other:

    Article Title: A spatial transcriptomic atlas of the host response to oropharyngeal candidiasis.
    Article Snippet: Spatial transcriptomics of resolving OPC identifies four major tissue compart ments in uninfected and infected tongue To analyze the microenvironment during OPC, we employed the 10× Genomics Visium spatial transcriptomics technology on frozen tissue sections (n = 4) from tongues of normal and C. albicans-infected Balb/c mice at 60 h of OPC (hereby referred to as day 2, for ease of representation).

    Article Title: Visium Spatial Transcriptomics technology pipeline from 9/10 participants at biopsy 1. Using the ChimericSeq SoftwareTM, HBV-human chimeric reads that are indicative of mRNA transcribed from integrated HBV DNA were moved forward for analysis: all non-chimeric
    Article Snippet: To confirm that our 3’ HBV amplicon would exclude iDNA-derived transcripts, we identified viral junctions by performing RNA sequencing on permeabilized liver tissue through the 10x Visium Spatial Transcriptomics technology pipeline from 9/10 participants at biopsy 1.

    Mouse Assay:

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. ( A ) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. ( B ) Heatmap of top differentially expressed genes for each spatial domain. ..

    Gene Expression:

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. ( A ) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. ( B ) Heatmap of top differentially expressed genes for each spatial domain. ..

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice.
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. (A) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. (B) Heatmap of top differentially expressed genes for each spatial domain. ..

    Marker:

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. ( A ) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. ( B ) Heatmap of top differentially expressed genes for each spatial domain. ..

    Article Title: Molecular pathology of acute spinal cord injury in middle-aged mice.
    Article Snippet: .. Fig. 3 Spatial transcriptomics identifies distinct domains in and around the injury site that are similar between young and middle-aged mice. (A) 10X Visium spatial transcriptomic spots were clustered based on gene expression and mapped on the injury site to identify eight distinct spatial domains that were named based on a combination of marker genes, Gene Ontology terms, and spatial location. (B) Heatmap of top differentially expressed genes for each spatial domain. ..

    Biomarker Discovery:

    Article Title: Spatial and single cell mapping of castleman disease reveals key stromal cell types and cytokine pathways.
    Article Snippet: .. Spatial transcriptomics analysis of a validation cohort of CD We performed 10x Xenium spatial transcriptomics analysis in a validation cohort of 13 CD cases and controls. ..



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    10X Genomics xenium spatial transcriptome 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.
    Xenium Spatial Transcriptome Analysis, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    xenium in situ spatial transcriptomic analysis  (10X Genomics)
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    10X Genomics xenium in situ spatial transcriptomic 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.
    Xenium In Situ Spatial Transcriptomic Analysis, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    10x xenium spatial transcriptomics analysis  (Spatial Transcriptomics Inc)
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    Spatial Transcriptomics Inc 10x xenium spatial transcriptomics 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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    Average 90 stars, based on 1 article reviews
    10x xenium spatial transcriptomics analysis - by Bioz Stars, 2026-09
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    xenium-based spatial transcriptomics analysis  (Spatial Transcriptomics Inc)
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    Xenium-Based Spatial <t>Transcriptomics</t> 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
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    Image Search Results


    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

    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

    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