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visium spatial transcriptomics st  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc visium spatial transcriptomics st
    Visium Spatial Transcriptomics St, 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/visium+spatial+transcriptomics+sequencing+data/data+spatial+transcriptomics+visium/pm41592568-773-7-8
    Average 86 stars, based on 1 article reviews
    visium spatial transcriptomics st - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: Phase Separation Competent TIA1 Couples Glycolytic Shutdown to CD8 + T-Cell Activation and Shapes the Efficacy of Intravesical BCG in Bladder Cancer
    Article Snippet: .. Visium spatial-transcriptomics data (GEO GSE171351 ) were processed in Seurat v4; TIA1, EPCAM, and CD8A spot-level expression was visualized in ggplot2 (RStudio, Version: 2025.09.2+418). ..

    Article Title: A technical comparison of spatial transcriptomics platforms across six cancer types.
    Article Snippet: .. To systematically evaluate the technical performance of current spatial transcriptomics technologies, we profiled six FFPE tumor types using five commercially available platforms: Visium v1, Visium v2 (CytAssist), VisiumHD, Xenium, and CosMx. ..


    Article Title: Integrative transcriptomic analysis reveals microglial metabolic-inflammatory crosstalk of HK2–HSPA5–TNF axis after intracerebral hemorrhage
    Article Snippet: .. Spatial transcriptomics analysis leveraged preprocessed Visium data from lesional (hemorrhage-affected) and contralateral hemispheres across nine timepoints (Naive to D28). ..

    Article Title: Ghent Pathology 2025. 15th Joint Meeting of the BDIAP and The Pathological Society joint with the Belgian Society of Pathology, 24-26 June 2025.
    Article Snippet: .. Additionally, we assessed SEQUOIA’s ability to infer spatially resolved expression by comparing predicted values with ground truth obtained from Visium spatial transcriptomics data. ..

    Article Title: CEBPB expression in tumor cells drives immune evasion in colorectal cancer via CTLA4 upregulation in T cells
    Article Snippet: .. For comparative analyses, we also used the publicly available human colorectal cancer scRNA-seq dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178341) and a Visium spatial-transcriptomics dataset from Zenodo (https://doi.org/10.5281/zenodo.7551712). .. HJY, DY, JDL, HS, and SMK performed in vitro and in vivo experiments, CHP, KK, D ow nloaded from https://spj.science.org on February 04, 2026 32 and HS analyzed scRNA-seq data, HRS analyzed whole-exome sequencing, immunohistochemistry, and public data, CP analyzed public data, MJK, JWP, SBR, SYJ, KJP, and TYK provided human tumor tissue and analyzed clinical data, YL analyzed Lunit SCOPE IO data, JK supervised scRNA-seq analysis, JKW supervised public data and pathological analysis, and SWH provided concept of the study and supervised in vitro and in vivo experiments.

    Article Title: Hist2Cell: Deciphering fine-grained cellular architectures from histology images.
    Article Snippet: .. 39 We selected slices that included both Visium Spatial Transcriptomics (ST) data and 20× magnification H&E images. ..

    Article Title: Single Cell and Spatial Transcriptomics Define a Proinflammatory and Profibrotic Niche After Kidney Injury.
    Article Snippet: .. Spatial Transcriptomics VisiumData Processing: Mouse kidney samples stored in a frozen state were embedded withOCT compound and stored at −80 °C. .. For the preparation of sections for Visium Spatial Transcriptomics sequencing, samples were equilibrated at−18 °C and a 10 μmthick section was cut onto the active sequencing area (6 mm x 6 mm) of a spatial barcoded slide.

    Expressing:

    Article Title: Phase Separation Competent TIA1 Couples Glycolytic Shutdown to CD8 + T-Cell Activation and Shapes the Efficacy of Intravesical BCG in Bladder Cancer
    Article Snippet: .. Visium spatial-transcriptomics data (GEO GSE171351 ) were processed in Seurat v4; TIA1, EPCAM, and CD8A spot-level expression was visualized in ggplot2 (RStudio, Version: 2025.09.2+418). ..

    Article Title: Ghent Pathology 2025. 15th Joint Meeting of the BDIAP and The Pathological Society joint with the Belgian Society of Pathology, 24-26 June 2025.
    Article Snippet: .. Additionally, we assessed SEQUOIA’s ability to infer spatially resolved expression by comparing predicted values with ground truth obtained from Visium spatial transcriptomics data. ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: A technical comparison of spatial transcriptomics platforms across six cancer types.
    Article Snippet: .. To systematically evaluate the technical performance of current spatial transcriptomics technologies, we profiled six FFPE tumor types using five commercially available platforms: Visium v1, Visium v2 (CytAssist), VisiumHD, Xenium, and CosMx. ..



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    Spatial <t>Transcriptomics</t> in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA <t>sequencing</t> with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.
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    Spatial <t>Transcriptomics</t> in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA <t>sequencing</t> with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.
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    Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing, RNA Sequencing

    Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing

    Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Functional Assay, Expressing, RNA Sequencing

    Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing, Control, Muscles