Review



visium spatial transcriptomic  (10X Genomics)

 
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 86
      Buy from Supplier

    Structured Review

    10X Genomics visium spatial transcriptomic
    Visium Spatial Transcriptomic, 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
    https://www.bioz.com/product/visium+spatial+transcriptomics+sequencing+data/expression+gene+slides+spatial+visium/pm38589392-234-12-10
    Average 86 stars, based on 1 article reviews
    visium spatial transcriptomic - by Bioz Stars, 2026-10
    86/100 stars

    Images

    Related Articles

    Gene Expression:

    Article Title: Mapping neuro-vascular unit communications reveals distinct angiogenic programs across developing mouse brain regions.
    Article Snippet: .. Reactions were carried out with the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Reagent Kits according to the manufacturer’s protocol with recommended reagents (10X Genomics, 1000193 and 1000187). ..

    Article Title: A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.
    Article Snippet: .. 5′ gene expression (GEX) libraries, single-cell V(D)J libraries (10x Genomics, 1000255) and cell surface protein libraries were prepared according to the manufacturer’s protocols. .. Library quality was evaluated using an Agilent 2200 TapeStation, and final libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms.

    Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
    Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

    Single Cell:

    Article Title: A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.
    Article Snippet: .. 5′ gene expression (GEX) libraries, single-cell V(D)J libraries (10x Genomics, 1000255) and cell surface protein libraries were prepared according to the manufacturer’s protocols. .. Library quality was evaluated using an Agilent 2200 TapeStation, and final libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms.

    Article Title: Multilayer network approaches to omics data integration in digital twins for cancer research
    Article Snippet: .. This process requires the non-trivial development of new methods that capture salient information from either estimation of cell type proportions from bulk RNA-seq , or from single-cell spatial (Visium/Xenium) ( ) and non-spatial datasets (10x Genomics scRNA-seq/scATAC-seq) ( ). ..

    Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
    Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

    RNA Sequencing:

    Article Title: Multilayer network approaches to omics data integration in digital twins for cancer research
    Article Snippet: .. This process requires the non-trivial development of new methods that capture salient information from either estimation of cell type proportions from bulk RNA-seq , or from single-cell spatial (Visium/Xenium) ( ) and non-spatial datasets (10x Genomics scRNA-seq/scATAC-seq) ( ). ..

    Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
    Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

    other:

    Article Title: Melanoma cell states shape spatial tumor-immune ecosystems to dictate the efficacy of anti-PD1 immunotherapy.
    Article Snippet: Spatial transcriptomic data were generated by the CRCL (Cancer Research Center Of Lyon) Cancer Genomics Platform using Visium CytAssist Spatial gene expression for FFPE, Human Transcriptome, kit (10X Genomics), according to the manufacturer’s guidelines.



    Similar Products

    visium spatial transcriptomics sequencing data  (Spatial Transcriptomics Inc)
    90
    Spatial Transcriptomics Inc visium spatial transcriptomics sequencing data
    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.
    Visium Spatial Transcriptomics Sequencing Data, 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/visium+spatial+transcriptomics+sequencing+data/10x+spatial+transcriptomics/pmc11177202-313-0-1
    Average 90 stars, based on 1 article reviews
    visium spatial transcriptomics sequencing data - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier
    spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform  (10X Genomics)
    90
    10X Genomics spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform
    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.
    Spatial Transcriptome Rna Sequencing (Strna Seq) Data For Breast Cancer Samples, Specific To The 10x Visium Platform, supplied by 10X Genomics, 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/visium+spatial+transcriptomics+sequencing+data/cells+generated+with+the+10x+genomics+3%E2%80%99+v+2+protocol/pm38450906-83-9-20
    Average 90 stars, based on 1 article reviews
    spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    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