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Spatial Transcriptomics Inc spatial transcriptomics data analysis
Spatial Transcriptomics Data 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
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RNA Sequencing:

Article Title: Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.
Article Snippet: .. The most commonly used variants include bulk RNA-seq, single-cell RNA-seq (scRNA-seq), and spatial RNA-seq (spatial transcriptomics), as shown in (Fig. 1). ..

Article Title: Expression profile of GSDMB in oral squamous cell carcinoma and its impact on tumor immune microenvironment and prognosis.
Article Snippet: .. Spatial transcriptomics RNA-seq data from OSCC samples were analyzed using the "Seurat" package. ..

Article Title: Mapping the secondary response to traumatic brain injury using spatial transcriptomics shows acute 4-aminopyridine treatment mitigates axonal and molecular pathology.
Article Snippet: FFPE Immunohistochemistry: Coronal sections (7 μm) anterior to the spatial transcriptomics sections and under the TBI impact site were immunolabeled for myelin basic protein (MBP), β−APP, GFAP, or IBA1 (Table S2). .. Spatial Transcriptomics Data Analysis: Visium Spatial RNA-seq and microscope images were processed for all 24 mice using 10x Genomics Space Ranger analysis pipeline (v2.1.1) to align raw reads to the mouse reference genome and generate gene count by spot matrices aligned to corresponding tissue images. ..

Article Title: Experimental analysis of bone marrow adipose tissue and bone marrow adipocytes: An update from the bone marrow adiposity society (BMAS)
Article Snippet: .. Spatial transcriptomics RNA-seq can be performed on any histological section of adipose tissue. ..

Article Title: Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
Article Snippet: .. Raw sequencing data for single-nuclei RNA-seq and spatial transcriptomics RNA-seq generated in this study are deposited in the Gene Expression Omnibus (GEO) under the accession numbers: GSE306228 (single-nucleus RNA-seq data) and GSE306418 (Spatial Transcriptomics). .. Processed snRNA-seq data are available at the Broad Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) (SCP: SCP3248).

Article Title: Inferring causal trajectories from spatial transcriptomics using CASCAT
Article Snippet: .. Table S3: Summary of real Spatial Transcriptomics RNA-seq datasets used in this study. ..

other:

Article Title: TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses.
Article Snippet: Mouse prefrontal cortex: Spatial transcriptomics (STARmap) at ‘20180419_BZ9_control’ in https://www.starmapresources. com/data; RNA-seq (10x Chromium) at GSE158450 in the GEO for ‘PFC_sc_Rep2_10X’.

Spatial Transcriptomics:

Article Title: Expression profile of GSDMB in oral squamous cell carcinoma and its impact on tumor immune microenvironment and prognosis.
Article Snippet: .. Spatial transcriptomics RNA-seq data from OSCC samples were analyzed using the "Seurat" package. ..

Article Title: Mapping the secondary response to traumatic brain injury using spatial transcriptomics shows acute 4-aminopyridine treatment mitigates axonal and molecular pathology.
Article Snippet: FFPE Immunohistochemistry: Coronal sections (7 μm) anterior to the spatial transcriptomics sections and under the TBI impact site were immunolabeled for myelin basic protein (MBP), β−APP, GFAP, or IBA1 (Table S2). .. Spatial Transcriptomics Data Analysis: Visium Spatial RNA-seq and microscope images were processed for all 24 mice using 10x Genomics Space Ranger analysis pipeline (v2.1.1) to align raw reads to the mouse reference genome and generate gene count by spot matrices aligned to corresponding tissue images. ..

Article Title: Multiomics Integration for Identifying Treatment Targets, Drug Development, and Diagnostic Designs in PAH
Article Snippet: .. The newly developed spatial RNA-Seq technology (spatial transcriptomics) preserves the spatial context of RNA expression and maps gene expression within tissue architecture for comprehensive studies of biological systems. ..

Article Title: Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
Article Snippet: .. Raw sequencing data for single-nuclei RNA-seq and spatial transcriptomics RNA-seq generated in this study are deposited in the Gene Expression Omnibus (GEO) under the accession numbers: GSE306228 (single-nucleus RNA-seq data) and GSE306418 (Spatial Transcriptomics). .. Processed snRNA-seq data are available at the Broad Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) (SCP: SCP3248).

Article Title: Inferring causal trajectories from spatial transcriptomics using CASCAT
Article Snippet: .. Table S3: Summary of real Spatial Transcriptomics RNA-seq datasets used in this study. ..

Microscopy:

Article Title: Mapping the secondary response to traumatic brain injury using spatial transcriptomics shows acute 4-aminopyridine treatment mitigates axonal and molecular pathology.
Article Snippet: FFPE Immunohistochemistry: Coronal sections (7 μm) anterior to the spatial transcriptomics sections and under the TBI impact site were immunolabeled for myelin basic protein (MBP), β−APP, GFAP, or IBA1 (Table S2). .. Spatial Transcriptomics Data Analysis: Visium Spatial RNA-seq and microscope images were processed for all 24 mice using 10x Genomics Space Ranger analysis pipeline (v2.1.1) to align raw reads to the mouse reference genome and generate gene count by spot matrices aligned to corresponding tissue images. ..

RNA sequencing:

Article Title: Multiomics Integration for Identifying Treatment Targets, Drug Development, and Diagnostic Designs in PAH
Article Snippet: .. The newly developed spatial RNA-Seq technology (spatial transcriptomics) preserves the spatial context of RNA expression and maps gene expression within tissue architecture for comprehensive studies of biological systems. ..

RNA Expression:

Article Title: Multiomics Integration for Identifying Treatment Targets, Drug Development, and Diagnostic Designs in PAH
Article Snippet: .. The newly developed spatial RNA-Seq technology (spatial transcriptomics) preserves the spatial context of RNA expression and maps gene expression within tissue architecture for comprehensive studies of biological systems. ..

Gene Expression:

Article Title: Multiomics Integration for Identifying Treatment Targets, Drug Development, and Diagnostic Designs in PAH
Article Snippet: .. The newly developed spatial RNA-Seq technology (spatial transcriptomics) preserves the spatial context of RNA expression and maps gene expression within tissue architecture for comprehensive studies of biological systems. ..

Article Title: Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
Article Snippet: .. Raw sequencing data for single-nuclei RNA-seq and spatial transcriptomics RNA-seq generated in this study are deposited in the Gene Expression Omnibus (GEO) under the accession numbers: GSE306228 (single-nucleus RNA-seq data) and GSE306418 (Spatial Transcriptomics). .. Processed snRNA-seq data are available at the Broad Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) (SCP: SCP3248).

Sequencing:

Article Title: Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
Article Snippet: .. Raw sequencing data for single-nuclei RNA-seq and spatial transcriptomics RNA-seq generated in this study are deposited in the Gene Expression Omnibus (GEO) under the accession numbers: GSE306228 (single-nucleus RNA-seq data) and GSE306418 (Spatial Transcriptomics). .. Processed snRNA-seq data are available at the Broad Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) (SCP: SCP3248).

Generated:

Article Title: Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps
Article Snippet: .. Raw sequencing data for single-nuclei RNA-seq and spatial transcriptomics RNA-seq generated in this study are deposited in the Gene Expression Omnibus (GEO) under the accession numbers: GSE306228 (single-nucleus RNA-seq data) and GSE306418 (Spatial Transcriptomics). .. Processed snRNA-seq data are available at the Broad Single Cell Portal ( https://singlecell.broadinstitute.org/single_cell ) (SCP: SCP3248).



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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 <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