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spatial transcriptomic analysis  (10X Genomics)

 
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    10X Genomics spatial transcriptomic analysis
    Spatial Transcriptomic Analysis, 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/analysis+spatial+transcriptomics/visium/pm41517835-341-0-4
    Average 86 stars, based on 1 article reviews
    spatial transcriptomic analysis - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.
    Article Snippet: .. The typical evolution of spatial transcriptomics technologies is characterized by continuous improvement in spatial resolution, ranging from 10x Genomics Visium (55 μm spot resolution, AR TIC LE IN PR ES S capturing approximately 1-10 cells per spot) [5], to Slide-seq (~10 μm, near-cellular resolution) [6], and finally to Stereo-seq (0.22 μm, subcellular resolution) [7]. ..

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Article Title: GLP1-E2 therapy delays autoimmune diabetes in late-stage prediabetic NOD mice and potentiates low-dose anti-CD3 therapy for enhanced disease protection.
    Article Snippet: .. Analytically, we employed 10X Genomics Visium for spatial transcriptomics, which lacks true single-cell resolution compared with newer platforms such as Visium HD or Xenium. ..

    Article Title: Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.
    Article Snippet: .. Recently, spatial transcriptomics, especially Visium (10X genomics, USA), has been garnering significant attention in cancer research. ..

    Fluorescence:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    In Situ Hybridization:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Labeling:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Gene Expression:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    other:

    Article Title: Integrative single-cell and spatial multi-Omics analyses identify NETs-driven colon cancer subtypes with distinct metabolic features and prognostic implications.
    Article Snippet: ACC, Adrenocortical Carcinoma; ARRDC1, Arrestin Domain Containing 1; AUC, Area Under the Curve; AUCell, Area Under the Curve Cell-level scoring; BH, Benjamini–Hochberg; BLCA, Bladder Urothelial Carcinoma; AR TIC LE IN PR ES S BRCA, Breast Cancer; CESC, Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; CHOL, Cholangiocarcinoma; CI, Confidence Interval; CNV, Copy Number Variation; COAD, Colon Adenocarcinoma; CRC, Colorectal Cancer; CSS, Cancer-Specific Survival; CXCR4, C-X-C Chemokine Receptor Type 4; DEGs, Differentially Expressed Genes; DUSP5, Dual-Specificity Phosphatase 5; ELISA, Enzyme-Linked Immunosorbent Assay; eQTL, Expression Quantitative Trait Locus; ESCA, Esophageal Carcinoma; FDR, False Discovery Rate; GDSC, Genomics of Drug Sensitivity in Cancer; GEO, Gene Expression Omnibus; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; GWAS, Genome-Wide Association Study; HNSC, Head and Neck Squamous Cell Carcinoma; HPA, Human Protein Atlas; HR, Hazard Ratio; IC50, Half-Maximal Inhibitory Concentration; ICIs, Immune Checkpoint Inhibitors; KEGG, Kyoto Encyclopedia of Genes and Genomes; KICH, Kidney Chromophobe; KIRC, Kidney Renal Clear Cell Carcinoma; KM, Kaplan–Meier; AR TIC LE IN PR ES S LASSO, Least Absolute Shrinkage and Selection Operator; LGG, Low-Grade Glioma; LUAD, Lung Adenocarcinoma; MAPK, Mitogen-Activated Protein Kinase; MD, Molecular Dynamics; MESO, Mesothelioma; MIA, Multimodal Intersection Analysis; MIF, Macrophage Migration Inhibitory Factor; NETs, Neutrophil Extracellular Traps; OS, Overall Survival; PCA, Principal Component Analysis; READ, Rectal Adenocarcinoma; RMSD, Root Mean Square Deviation; ROC, Receiver Operating Characteristic; ROS, Reactive Oxygen Species; SARC, Sarcoma; scRNA-seq, Single-Cell RNA Sequencing; SLC2A3, Solute Carrier Family 2 Member 3; SNV, Single Nucleotide Variant; ssGSEA, Single-Sample Gene Set Enrichment Analysis; STAD, Stomach Adenocarcinoma; TAMs, Tumor-Associated Macrophages; TANs, Tumor-Associated Neutrophils; TCGA, The Cancer Genome Atlas; THCA, Thyroid Carcinoma; THYM, Thymoma; TIDE, Tumor Immune Dysfunction and Exclusion; TME, Tumor Microenvironment; TPM, Transcripts Per Million; AR TIC LE IN PR ES S Tregs, Regulatory T Cells; TUBB2A, Tubulin Beta Class 2A; UCEC, Uterine Corpus Endometrial Carcinoma; UMI, Unique Molecular Identifier; UVM, Uveal Melanoma; Visium, 10x Genomics Visium

    Single Cell:

    Article Title: GLP1-E2 therapy delays autoimmune diabetes in late-stage prediabetic NOD mice and potentiates low-dose anti-CD3 therapy for enhanced disease protection.
    Article Snippet: .. Analytically, we employed 10X Genomics Visium for spatial transcriptomics, which lacks true single-cell resolution compared with newer platforms such as Visium HD or Xenium. ..

    Expressing:

    Article Title: SpatialBench : Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue
    Article Snippet: .. The original Visium (10x Genomics) became the most widely adopted sST platform ( ) , offering transcriptome-wide coverage while aggregating expression from multiple cells per 55 μm resolution that aggregates expression from multiple cells per spot ( , ) . ..



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    spatial transcriptomics data analysis - by Bioz Stars, 2026-09
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    a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Journal: bioRxiv

    Article Title: CXCL10 drives female-specific tau pathology progression and defines sex-dependent vulnerability in tauopathy model mice

    doi: 10.64898/2026.04.19.719088

    Figure Lengend Snippet: a Schematic diagram of the spatial transcriptome analysis using Xenium Prime 5K. Formalin fixed paraffin embedded (FFPE) sections were prepared from 12-month-old Tau Tg mice and age-matched WT controls. b UMAP visualizing the cell cluster detected by Xenium in the brains of Tau Tg and WT mice. Neuronal cells were classified as IT (intratelencephalic), ET (extratelencephalic), Glut (glutamatergic), NP (near-projecting), CT (corticothalamic), L6b (layer 6b), DG (dentate gyrus), IMN (immature neurons), CTX (cerebral cortex), CGE (caudal ganglionic eminence), GABA (GABAergic), MGE (medial ganglionic eminence), CNU (cerebral nuclei), LGE (lateral ganglionic eminence), Hya (anterior hypothalamic), HY (hypothalamus), MM (medial mammillary nucleus), LH (lateral habenula), TH (thalamus), MB (midbrain), HB (hindbrain), Sero (serotonergic), MY (medulla), NN (non-neuronal), NP (near-projecting), OB (olfactory bulb), OEC (olfactory ensheathing cells), and OLF (olfactory areas). c Cxcl10 mRNA signal was plotted using Feature Plot on UMAP. d Quantitative Cxcl10 gene expression using violin plots in AC-Epen, BAM, DG-IMN Glut, IT-ET Glut, MG, and T cell types. e, h Representative plots of the result of re-clustering AC-Epen ( e ) and immune cluster ( h ), respectively. f Plots of Cxcl10 + cells in the cluster shown in and represented according to genotype. g, j Figures showing spatial distribution of AC8 ( g ) and MG3 ( j ) clusters in the brains of WT and Tau Tg mice. k Representative images of coronal section of mouse brain by Xenium explorer. Scale bar = 1 mm. l Spatial information of Cxcl10 + astrocytes and microglia in the hippocampus of Tau Tg mice using Xenium explorer. Scale bar = 100 μm. Number of mice used: male WT (n = 1), male Tau Tg (n = 1), female WT (n = 1), and female Tau Tg (n = 1). Statistical analysis was performed using a Wilcoxon rank sum U statistic test ( d ). Source data are provided in the Source Data file.

    Article Snippet: FFPE brain sections were analyzed using Xenium spatial transcriptome analysis (10x Genomics).

    Techniques: Formalin-fixed Paraffin-Embedded, Olfactory, Gene Expression