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rna capture based approaches  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc rna capture based approaches
    Rna Capture Based Approaches, 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/capture+phase+rna+solid/pmc12694334-83-7-0
    Average 86 stars, based on 1 article reviews
    rna capture based approaches - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: Spatiotemporal transcriptomic mapping reveals region-specific glial activation and astrocyte shifts in epileptogenesis beyond the hippocampus.
    Article Snippet: .. Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J (2018) Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. ..

    Article Title: Development and Application of Single Cell Multi-omics Methods for Complex Disease
    Article Snippet: .. Salmén, F. et al. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. ..

    Article Title: A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
    Article Snippet: .. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. ..

    Article Title: Spatial Dissection of the Immune Landscape of Solid Tumors to Advance Precision Medicine
    Article Snippet: .. Spatial transcriptomics techniques A. Spatial indexing approaches, distinguished in solid-phase capture (left) and deterministic barcoding (right). ..

    Imaging:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..

    Fluorescence:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..

    In Situ Hybridization:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..

    Fluorescence In Situ Hybridization:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..

    In Situ:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..

    Labeling:

    Article Title: Single-Cell Omics in Legumes: Research Trends and Applications
    Article Snippet: .. Spatial transcriptomics can be categorized into (1) RNA capture-based approaches (e.g., 10× Visium, Slide-seq) where tissue sections are placed on slides patterned with spatially barcoded primers that capture RNA molecules and tag them to record their spatial locations; (2) in probe- or imaging-based approaches [e.g., multiplexed error-robust fluorescence in situ hybridization (MERFISH), sequential FISH (seqFISH), Xenium in situ], where fluorescently labeled probes hybridize target transcripts on a tissue cross-section, enabling direct visualization of transcripts locations at high spatial resolution [ ]. ..



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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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    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