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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/spatial+transcriptome+sequencing+visium+platform/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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    (A) Experimental workflow for, and analysis of, single-cell <t>transcriptome</t> (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.
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    Image Search Results


    (A) Experimental workflow for, and analysis of, single-cell transcriptome (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.

    Journal: bioRxiv

    Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

    doi: 10.1101/2023.08.18.553804

    Figure Lengend Snippet: (A) Experimental workflow for, and analysis of, single-cell transcriptome (scRNA-seq) and spatial transcriptome (ST-seq) of gill tissue in fully symbiotic (InS group) and partially decolonized (DeC) deep-sea mussels. A marked decrease of the endosymbiont is observed after in situ translocation assay (n=14 for the InS group, n=5 for the DeC group). (B) t-SNE projection of spatial transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Projection of cell clusters onto spatial transcriptome barcoded spots (right) in the InS group. Two successive sections were used in the same capture region of spatial transcriptome as technique replicates. (C) t-SNE projection of single-cell transcriptome clustered by gene expression in the InS group, with color assigned by cell type (left). Spatial transcriptome barcoded spots labeled using scRNA-seq cell type with maximum prediction score (right). (D) Fluorescent in situ hybridization (FISH) of endosymbionts with successive gill sections for ST-seq (InS group) and ISH of bacteriocytes marker genes.

    Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

    Techniques: In Situ, Translocation Assay, Gene Expression, Labeling, In Situ Hybridization, Marker

    (A) ScRNA/ST-seq and meta-transcriptome data show an intimate interaction of sterol metabolism between the host and symbionts. In support of this, immunofluorescence (IF) assay (using gills of the InS group) of the 24-hydroxycholesterol 7 alpha-hydroxylase (CYP39A1) protein shows that CYP39A1 proteins are widely distributed across bacteriocytes. In addition, a more intensive signal of CYP39A1 protein could also be observed at the apical region that enriched with endosymbionts (indicated by lipid A signals). (B) ScRNA/ST-seq and meta-transcriptome data show intimate interaction of glucose/glycogen metabolism between the host and symbionts. In support of this, IF assay of the sugar phosphate exchanger (SLC37A2) protein shows the co-location of SLC37A2 proteins with endosymbionts inside bacteriocytes. (C) ScRNA/ST-seq and meta-transcriptome data show intimate interactions of ammonia metabolism between the host and symbionts. In support of this, IF assay of the ammonium transporter Rh (RHBG-A) protein shows co-location of RHBG-A proteins with endosymbionts inside bacteriocytes.

    Journal: bioRxiv

    Article Title: Cooperation between bacteriocytes and endosymbionts drives function and development of symbiotic cells in mussel holobionts

    doi: 10.1101/2023.08.18.553804

    Figure Lengend Snippet: (A) ScRNA/ST-seq and meta-transcriptome data show an intimate interaction of sterol metabolism between the host and symbionts. In support of this, immunofluorescence (IF) assay (using gills of the InS group) of the 24-hydroxycholesterol 7 alpha-hydroxylase (CYP39A1) protein shows that CYP39A1 proteins are widely distributed across bacteriocytes. In addition, a more intensive signal of CYP39A1 protein could also be observed at the apical region that enriched with endosymbionts (indicated by lipid A signals). (B) ScRNA/ST-seq and meta-transcriptome data show intimate interaction of glucose/glycogen metabolism between the host and symbionts. In support of this, IF assay of the sugar phosphate exchanger (SLC37A2) protein shows the co-location of SLC37A2 proteins with endosymbionts inside bacteriocytes. (C) ScRNA/ST-seq and meta-transcriptome data show intimate interactions of ammonia metabolism between the host and symbionts. In support of this, IF assay of the ammonium transporter Rh (RHBG-A) protein shows co-location of RHBG-A proteins with endosymbionts inside bacteriocytes.

    Article Snippet: Only one mussel from the InS group was used for single cell transcriptome sequencing (scRNA-seq, Chromium platform of 10x Genomics, Pleasanton CA, USA) and spatial transcriptome sequencing (ST-seq, Visium platform of 10x Genomics), and all 14 mussels collected by isothermal isobaric sampler or after RNA stabilizing treatment were subjected to meta-transcriptome sequencing.

    Techniques: Immunofluorescence