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Spatial Transcriptomics Inc xenium-based spatial transcriptomics analysis
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
Xenium Based 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/based+transcriptome+analysis/spatial+transcriptomics++st+/pmc11396644-186-3-3
Average 90 stars, based on 1 article reviews
xenium-based spatial transcriptomics analysis - by Bioz Stars, 2026-09
90/100 stars

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1) Product Images from "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"

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

Journal: Biomarker Research

doi: 10.1186/s40364-024-00636-3

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
Figure Legend 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

Techniques Used: Control, Expressing, Marker

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Gene Expression:

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Histopathology:

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Article Title: An integrated single-cell reference atlas of the human endometrium
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Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
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Article Title:
Article Snippet: B266/P1991 Imaging-based spatial transcriptomics technology identifies predictive biomarkers for relapse in colon cancer stage II.

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
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Comparison:

Article Title: STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
Article Snippet: Spatial transcriptomics (ST) technologies have enabled gene expression profiling in the native spatial context of tissues.

Article Title: An integrated single-cell reference atlas of the human endometrium
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Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) technologies have revolutionized the understanding of spatially informed gene expression, which provide invaluable insights into the molecular architecture of complex diseases such as Alzheimer disease (AD).

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the stromal cell states present in the human endometrium, we used the same approach described in Supplementary Note 3 for the annotation of epithelial cells which considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 3b).

Article Title: Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Article Snippet: Additionally, the size of features in image-based spatial transcriptomics technologies has increased from 30 to 10,000 , making it increasingly feasible to use deep learning models.

Article Title: Centrosome-, mitotic spindle- and cytokinetic bridge-specific compartmentalization of AGO2 protein in human liver cells undergoing mitosis: Non-canonical, RNAi-dependent, control of local homeostasis
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Article Title:
Article Snippet: B266/P1991 Imaging-based spatial transcriptomics technology identifies predictive biomarkers for relapse in colon cancer stage II.

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) data provide spatially informed gene expression profiles.

Expressing:

Article Title: STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
Article Snippet: Spatial transcriptomics (ST) technologies have enabled gene expression profiling in the native spatial context of tissues.

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the epithelial cell states present in the human endometrium we considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 2a & Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 2b-f and Extended Data Fig. 7).

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) technologies have revolutionized the understanding of spatially informed gene expression, which provide invaluable insights into the molecular architecture of complex diseases such as Alzheimer disease (AD).

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the stromal cell states present in the human endometrium, we used the same approach described in Supplementary Note 3 for the annotation of epithelial cells which considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 3b).

Article Title: Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Article Snippet: Additionally, the size of features in image-based spatial transcriptomics technologies has increased from 30 to 10,000 , making it increasingly feasible to use deep learning models.

Article Title: Centrosome-, mitotic spindle- and cytokinetic bridge-specific compartmentalization of AGO2 protein in human liver cells undergoing mitosis: Non-canonical, RNAi-dependent, control of local homeostasis
Article Snippet: Spatial transcriptomics-mediated profiling of the mRNA/siRNA species populating either TRBP2 +/+ or TRBP2 −/− MEF-residing centrosomes in dividing/mitotic vs. interphase cells may indicate TRBP2-independent centrosome-specific RNAi machinery that functions non-canonically during mitosis.

Article Title:
Article Snippet: B266/P1991 Imaging-based spatial transcriptomics technology identifies predictive biomarkers for relapse in colon cancer stage II.

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) data provide spatially informed gene expression profiles.

Marker:

Article Title: STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
Article Snippet: Spatial transcriptomics (ST) technologies have enabled gene expression profiling in the native spatial context of tissues.

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the epithelial cell states present in the human endometrium we considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 2a & Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 2b-f and Extended Data Fig. 7).

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) technologies have revolutionized the understanding of spatially informed gene expression, which provide invaluable insights into the molecular architecture of complex diseases such as Alzheimer disease (AD).

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the stromal cell states present in the human endometrium, we used the same approach described in Supplementary Note 3 for the annotation of epithelial cells which considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 3b).

Article Title: Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Article Snippet: Additionally, the size of features in image-based spatial transcriptomics technologies has increased from 30 to 10,000 , making it increasingly feasible to use deep learning models.

Article Title: Centrosome-, mitotic spindle- and cytokinetic bridge-specific compartmentalization of AGO2 protein in human liver cells undergoing mitosis: Non-canonical, RNAi-dependent, control of local homeostasis
Article Snippet: Spatial transcriptomics-mediated profiling of the mRNA/siRNA species populating either TRBP2 +/+ or TRBP2 −/− MEF-residing centrosomes in dividing/mitotic vs. interphase cells may indicate TRBP2-independent centrosome-specific RNAi machinery that functions non-canonically during mitosis.

Article Title:
Article Snippet: B266/P1991 Imaging-based spatial transcriptomics technology identifies predictive biomarkers for relapse in colon cancer stage II.

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) data provide spatially informed gene expression profiles.

Single-cell Transcriptomics:

Article Title: STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition
Article Snippet: Spatial transcriptomics (ST) technologies have enabled gene expression profiling in the native spatial context of tissues.

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the epithelial cell states present in the human endometrium we considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 2a & Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 2b-f and Extended Data Fig. 7).

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) technologies have revolutionized the understanding of spatially informed gene expression, which provide invaluable insights into the molecular architecture of complex diseases such as Alzheimer disease (AD).

Article Title: An integrated single-cell reference atlas of the human endometrium
Article Snippet: To annotate the stromal cell states present in the human endometrium, we used the same approach described in Supplementary Note 3 for the annotation of epithelial cells which considered: (i) the distinctive expression of genes, including bona fide markers (Fig. 3a), (ii) the menstrual stage at which these cells appear (Fig. 1f), and (iii) their spatial coordinates, as inferred by integrating single-cell transcriptomics with Spatial Transcriptomics (Visium) (Fig. 3b).

Article Title: Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings
Article Snippet: Additionally, the size of features in image-based spatial transcriptomics technologies has increased from 30 to 10,000 , making it increasingly feasible to use deep learning models.

Article Title: Centrosome-, mitotic spindle- and cytokinetic bridge-specific compartmentalization of AGO2 protein in human liver cells undergoing mitosis: Non-canonical, RNAi-dependent, control of local homeostasis
Article Snippet: Spatial transcriptomics-mediated profiling of the mRNA/siRNA species populating either TRBP2 +/+ or TRBP2 −/− MEF-residing centrosomes in dividing/mitotic vs. interphase cells may indicate TRBP2-independent centrosome-specific RNAi machinery that functions non-canonically during mitosis.

Article Title:
Article Snippet: B266/P1991 Imaging-based spatial transcriptomics technology identifies predictive biomarkers for relapse in colon cancer stage II.

Article Title: Integrating spatial transcriptomics and snRNA-seq data enhances differential gene expression analysis results of AD-related phenotypes
Article Snippet: Spatial transcriptomics (ST) data provide spatially informed gene expression profiles.



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Image Search Results


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