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spatial transcriptomics st  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc spatial transcriptomics st
    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+transcriptomics+st/visium/pmc12857762-212-0-0
    Average 86 stars, based on 1 article reviews
    spatial transcriptomics st - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Preserving:

    Article Title: The Spatiotemporal Heterogeneity of Tumor-Associated Stromal Cells: Reprogramming Plasticity to Unlock Precision Cancer Immunotherapy
    Article Snippet: .. Spatial transcriptomics (ST) and its derivative platforms (e.g., Visium, MERSCOPE, CosMx, and Stereo-seq) provide insights into the cellular ecological niche of the TME while preserving spatial topological information [ ]. ..

    Spatial Transcriptomics:

    Article Title: Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data
    Article Snippet: .. To ensure a comprehensive representation of major current Spatial Transcriptomics platforms, we chose 10 datasets from Visium, including a Mouse Olfactory Bulb study ( Ståhl et al. 2016 ), an Ovarian Cancer study ( Sanders et al. 2022 ), and a Breast Cancer study ( Andersson et al. 2021 ). .. We also included 12 datasets from MERFISH (Vizgen) on the Mouse Brain Hypothalamic region ( Moffitt et al. 2018 ), 10 datasets from Xenium on the human kidney ( Benjamin et al. 2024 ) and Mouse Brain Anterior Thalamic Nuclei (ATN) ( Kapustina et al. 2024 ), and 20 datasets from CosMx (Nanostring) on human Non-Small Cell Lung Cancer (NSCLC) ( He et al. 2022 ).

    Article Title: Spatiotemporal transcriptomic mapping reveals region-specific glial activation and astrocyte shifts in epileptogenesis beyond the hippocampus.
    Article Snippet: .. We collected brains from both rodent lithium-pilocarpine-induced SE rats and lithium-control counterparts to apply the Visium spatial transcriptomics technology. ..

    Article Title: Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology
    Article Snippet: Cells were then stained with trypan blue (Thermo Fisher Scientific) and enumerated using an automated cell counter (Bio-Rad) or a manual counter (Kova). .. Spatial transcriptomics (Visium) samples: A section of lung was cut and transferred to 10% buffered formalin to fix for 24 h, then transferred to 70% ethanol until wax embedding. ..

    Olfactory:

    Article Title: Adding highly variable genes to spatially variable genes can improve cell type clustering performance in spatial transcriptomics data
    Article Snippet: .. To ensure a comprehensive representation of major current Spatial Transcriptomics platforms, we chose 10 datasets from Visium, including a Mouse Olfactory Bulb study ( Ståhl et al. 2016 ), an Ovarian Cancer study ( Sanders et al. 2022 ), and a Breast Cancer study ( Andersson et al. 2021 ). .. We also included 12 datasets from MERFISH (Vizgen) on the Mouse Brain Hypothalamic region ( Moffitt et al. 2018 ), 10 datasets from Xenium on the human kidney ( Benjamin et al. 2024 ) and Mouse Brain Anterior Thalamic Nuclei (ATN) ( Kapustina et al. 2024 ), and 20 datasets from CosMx (Nanostring) on human Non-Small Cell Lung Cancer (NSCLC) ( He et al. 2022 ).

    Modification:

    Article Title: Spatial transcriptional profiling of CHB liver biopsies reveals an undetected population of zonally biased HBV-integrated cells.
    Article Snippet: .. 6 Methods: Modified Visium Spatial Transcriptomics (ST) and Single Nuclei RNASeq (snRNASeq) 7 were performed on 4 commercial HBV+ biopsies, and 6 liver biopsies from the clinical trial GS-8 US-174-0149. mIF for HBV viral proteins and CISH for HBV RNA and DNA were also performed. ..

    RNA sequencing:

    Article Title: Spatial transcriptional profiling of CHB liver biopsies reveals an undetected population of zonally biased HBV-integrated cells.
    Article Snippet: .. 6 Methods: Modified Visium Spatial Transcriptomics (ST) and Single Nuclei RNASeq (snRNASeq) 7 were performed on 4 commercial HBV+ biopsies, and 6 liver biopsies from the clinical trial GS-8 US-174-0149. mIF for HBV viral proteins and CISH for HBV RNA and DNA were also performed. ..

    Chromogenic In Situ Hybridization:

    Article Title: Spatial transcriptional profiling of CHB liver biopsies reveals an undetected population of zonally biased HBV-integrated cells.
    Article Snippet: .. 6 Methods: Modified Visium Spatial Transcriptomics (ST) and Single Nuclei RNASeq (snRNASeq) 7 were performed on 4 commercial HBV+ biopsies, and 6 liver biopsies from the clinical trial GS-8 US-174-0149. mIF for HBV viral proteins and CISH for HBV RNA and DNA were also performed. ..

    Fluorescence:

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [ , ]. ..

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    In Situ Hybridization:

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [ , ]. ..

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    Gene Expression:

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [ , ]. ..

    Article Title: Understanding and Advancing Wound Healing in the Era of Multi-Omic Technology.
    Article Snippet: .. Spatial transcriptomics platforms such as 10× Visium, Slide-seq, and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) preserve tissue architecture while capturing spatially resolved gene expression profiles, enabling the identification of spatial gradients in inflammatory signaling, revascularization, and epidermal regeneration [66,67]. ..

    Article Title: Transcriptomics in solanaceous crop improvement: advances and opportunities
    Article Snippet: .. Spatial transcriptomics technologies, including Visium, Slide-seq, and emerging in situ sequencing methods preserve tissue architecture while profiling spatially resolved gene expression, enabling reconstruction of cell-type-specific expression programs without physical cell isolation. ..

    In Situ:

    Article Title: Transcriptomics in solanaceous crop improvement: advances and opportunities
    Article Snippet: .. Spatial transcriptomics technologies, including Visium, Slide-seq, and emerging in situ sequencing methods preserve tissue architecture while profiling spatially resolved gene expression, enabling reconstruction of cell-type-specific expression programs without physical cell isolation. ..

    Sequencing:

    Article Title: Transcriptomics in solanaceous crop improvement: advances and opportunities
    Article Snippet: .. Spatial transcriptomics technologies, including Visium, Slide-seq, and emerging in situ sequencing methods preserve tissue architecture while profiling spatially resolved gene expression, enabling reconstruction of cell-type-specific expression programs without physical cell isolation. ..

    Expressing:

    Article Title: Transcriptomics in solanaceous crop improvement: advances and opportunities
    Article Snippet: .. Spatial transcriptomics technologies, including Visium, Slide-seq, and emerging in situ sequencing methods preserve tissue architecture while profiling spatially resolved gene expression, enabling reconstruction of cell-type-specific expression programs without physical cell isolation. ..

    Cell Isolation:

    Article Title: Transcriptomics in solanaceous crop improvement: advances and opportunities
    Article Snippet: .. Spatial transcriptomics technologies, including Visium, Slide-seq, and emerging in situ sequencing methods preserve tissue architecture while profiling spatially resolved gene expression, enabling reconstruction of cell-type-specific expression programs without physical cell isolation. ..



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    Image Search Results


    Spatial organization and cell-cell communication networks in the tumor microenvironment. (A–C) The developmental trajectories of cell sub-populations from a spatial perspective are investigated. (D, E) Heatmap and network diagrams displaying cell–cell dependency analysis in the colocated, neighboring, and extended neighboring (15-point) regions of the spatial transcriptomics data. (F) The interaction heatmap visualized the intensity of intercellular interactions mediated by the ligand-receptor pairs. (G) The spatial cell communication network diagram illustrates that NUhighepi exhibit a higher intensity of cell communication with other cells. (H) Circos plot summarizing cell-type-specific interaction patterns.

    Journal: Frontiers in Oncology

    Article Title: Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment

    doi: 10.3389/fonc.2025.1703778

    Figure Lengend Snippet: Spatial organization and cell-cell communication networks in the tumor microenvironment. (A–C) The developmental trajectories of cell sub-populations from a spatial perspective are investigated. (D, E) Heatmap and network diagrams displaying cell–cell dependency analysis in the colocated, neighboring, and extended neighboring (15-point) regions of the spatial transcriptomics data. (F) The interaction heatmap visualized the intensity of intercellular interactions mediated by the ligand-receptor pairs. (G) The spatial cell communication network diagram illustrates that NUhighepi exhibit a higher intensity of cell communication with other cells. (H) Circos plot summarizing cell-type-specific interaction patterns.

    Article Snippet: Breast cancer spatial transcriptomics (ST) data were acquired from the GEO database ( https://www.ncbi.nlm.nih.gov/geo/ ) and 10x Genomics official website ( https://www.10xgenomics.com/ ).

    Techniques:

    Salus-STS high-resolution spatial transcriptomics enables effective cell identification at the subcellular level. (A) Schematics illustrating of the study. (B) Results of cell segmentation via the Salus Cellbins Algorithm. (C–F) Distributions and medians (red text in the figures) of the area (in pixel 2 ) (C) , UMI counts (D) , gene numbers (E) , and proportions of mitochondrial UMIs (F) of segmented cellbins.

    Journal: Frontiers in Reproductive Health

    Article Title: Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes

    doi: 10.3389/frph.2025.1747902

    Figure Lengend Snippet: Salus-STS high-resolution spatial transcriptomics enables effective cell identification at the subcellular level. (A) Schematics illustrating of the study. (B) Results of cell segmentation via the Salus Cellbins Algorithm. (C–F) Distributions and medians (red text in the figures) of the area (in pixel 2 ) (C) , UMI counts (D) , gene numbers (E) , and proportions of mitochondrial UMIs (F) of segmented cellbins.

    Article Snippet: In this study, we used Salus-STS high-resolution spatial transcriptomics (∼1 μm resolution) and Salus Cellbins Algorithm to characterize the spatial transcriptomic profile of mouse testes at single-cell level.

    Techniques:

    Cellbin-based analysis enables accurate identification of distinct cell types in the mouse testis. (A) RCTD-annotated distinct cell types and their proportions. (B) UMAP visualization of the Salus-STS Cellbin data with scRNA-Seq data. (C) Spatial distribution of distinct cell types in the mouse testis. (D) Integrated distribution map of cell distributions in the mouse testis. (E) Markers of distinct cell types and their expression levels. Scaled expression: the average expression level scaled across genes to eliminate the effect of total expression level differences among genes. Percentage: for each cell type, the percentage of cellbins that express the specific gene out of all cellbins of the same type.

    Journal: Frontiers in Reproductive Health

    Article Title: Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes

    doi: 10.3389/frph.2025.1747902

    Figure Lengend Snippet: Cellbin-based analysis enables accurate identification of distinct cell types in the mouse testis. (A) RCTD-annotated distinct cell types and their proportions. (B) UMAP visualization of the Salus-STS Cellbin data with scRNA-Seq data. (C) Spatial distribution of distinct cell types in the mouse testis. (D) Integrated distribution map of cell distributions in the mouse testis. (E) Markers of distinct cell types and their expression levels. Scaled expression: the average expression level scaled across genes to eliminate the effect of total expression level differences among genes. Percentage: for each cell type, the percentage of cellbins that express the specific gene out of all cellbins of the same type.

    Article Snippet: In this study, we used Salus-STS high-resolution spatial transcriptomics (∼1 μm resolution) and Salus Cellbins Algorithm to characterize the spatial transcriptomic profile of mouse testes at single-cell level.

    Techniques: Expressing

    High-resolution spatial transcriptomics uncovers spatiotemporal markers of spermatogenesis. (A) Pseudotime trajectory analysis. (B) Randomly selected seminiferous tubules. (C,D) Top 6 genes with expression levels positively (C) and negatively (D) correlated with the axis from the tubule basement membrane (epithelium) to the lumen center respectively.

    Journal: Frontiers in Reproductive Health

    Article Title: Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes

    doi: 10.3389/frph.2025.1747902

    Figure Lengend Snippet: High-resolution spatial transcriptomics uncovers spatiotemporal markers of spermatogenesis. (A) Pseudotime trajectory analysis. (B) Randomly selected seminiferous tubules. (C,D) Top 6 genes with expression levels positively (C) and negatively (D) correlated with the axis from the tubule basement membrane (epithelium) to the lumen center respectively.

    Article Snippet: In this study, we used Salus-STS high-resolution spatial transcriptomics (∼1 μm resolution) and Salus Cellbins Algorithm to characterize the spatial transcriptomic profile of mouse testes at single-cell level.

    Techniques: Expressing, Membrane