visium datasets  (Spatial Transcriptomics Inc)

Journal: Journal of Medical Virology

Article Title: Dissecting Sex‐Specific Pathology in K18‐hACE2 Transgenic Mice Infected With Different SARS‐CoV‐2 Variants

doi: 10.1002/jmv.70506

Figure Lengend Snippet: Sex‐specific spatial transcriptomics analysis in Delta‐infected mouse lungs. Lungs from Delta‐infected female and male mice on 3‐ and 5‐days post infection (dpi) were processed for spatial transcriptomics. (A). H&E staining. (B) Spatial plots with dimensional reduction clustering overlay with individual clusters coded by color and each dot representing a capture spot. (C) Relative expression frequency of gene clusters across each sample in a bar plot. (D) Conserved gene markers in identified clusters shown in a dot plot with average gene expression denoted by a color (red = upregulated, blue = downregulated) and percent expression denoted by the size of a dot. (E) UMAP plots for individual samples with 6 identified major clusters. Each dot in the UMAP plots represents one of 1,317 ± 136 capture spots per sample shown in B and color denotes corresponding gene expression cluster.

Article Snippet: Spatial transcriptomics spots represent 55 mm diameter spots for spatially mapped bulk‐sequencing of all cells within a particular spot and spot clusters were defined using resolution = 0.12 expression profiles and spatial location.

Techniques: Infection, Staining, Expressing, Gene Expression

Journal: Journal of Medical Virology

Article Title: Dissecting Sex‐Specific Pathology in K18‐hACE2 Transgenic Mice Infected With Different SARS‐CoV‐2 Variants

doi: 10.1002/jmv.70506

Figure Lengend Snippet: Differential analysis of spatial transcriptomics identified gene markers within the lung immune cell clusters. Lungs from Delta‐infected female and male mice on 3‐ and 5‐days post infection (dpi) were analyzed by spatial transcriptomics. (A) Top 50 genes that are significantly associated with female (left) or male (right) ‘ImmuneCell’ cluster (presented in Figure ) in a dot plot with average gene expression denoted by a color (red = upregulated, blue = downregulated) and percent expression denoted by the size of a dot. (B) Gene expression of Gbp4, Psmb10, Saa3, or Fth1 in violin plot. (C) Spatially mapped gene expression of Gbp4, Psmb10, Saa3, or Fth1 on 3‐dpi. (D) Top 15 enriched pathways for female (left) and male (right) samples identified by gene ontology analysis.

Article Snippet: Spatial transcriptomics spots represent 55 mm diameter spots for spatially mapped bulk‐sequencing of all cells within a particular spot and spot clusters were defined using resolution = 0.12 expression profiles and spatial location.

Techniques: Infection, Gene Expression, Expressing

Journal: BMC Bioinformatics

Article Title: SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics

doi: 10.1186/s12859-025-06209-x

Figure Lengend Snippet: SCNT testing on human kidney 10X visium HD dataset. ( A ) Spatial clustering plot based on stPlot showing the distribution of 12 cell clusters across the entire tissue space. ( B ) Spatial distribution of the 12 cell clusters within a sub-region. ( C ) scFeature plot displaying the spatial expression feature of LRP2 within the sub-region

Article Snippet: To demonstrate the functionality of SCNT , we applied it to a 10X Genomics Visium HD dataset of human kidney tissue, following the official tutorial, including dimensionality reduction and clustering.

Techniques: Expressing

Journal: Genome Biology

Article Title: DeepGFT: identifying spatial domains in spatial transcriptomics of complex and 3D tissue using deep learning and graph Fourier transform

doi: 10.1186/s13059-025-03631-5

Figure Lengend Snippet: DeepGFT effectively characterized the subtle tissue architectures of human lymph node Visium data. a H&E image and ground truth segmentation of germinal center. b Domain assignments (evaluated by Jaccard index) and results generated by DeepGFT, BayesSpace, SpaGCN, SpaceFlow, Scanpy, GraphST, STAGATE, stLearn, SpatialPCA, and spaVAE in human lymph node section. c Evaluation results of four metrics (Jaccard index, precision, recall, and F1 score) of ten tools. d The GCs and their adjacent regions obtained from DeepGFT, as well as genes supported corresponding spatial domains. e Cell type compositions of each spatial domain, obtained from cell2location. f Biological processes involved in DEGs in domain 1

Article Snippet: The human lymph node dataset (10x Visium) is available at ( https://www.10xgenomics.com/cn/resources/datasets/human-lymph-node-1-standard-1-1-0 ) [ ].

Techniques: Generated

Journal: Discover Oncology

Article Title: Dissecting PTPN7‐driven aggressiveness in IDH‐wildtype astrocytomas: multi‐omics, clinical validation, and spatial transcriptomics for prognostic insights

doi: 10.1007/s12672-025-02662-5

Figure Lengend Snippet: Immunohistochemical quantification of PTPN7 in normal brain and gliomas. A TCGA proteomic analysis confirmed elevated PTPN7 expression in glioblastoma over normal tissue. B Summary table of PTPN7 density (mean ± SD) in normal tissue (n = 11) and IDH‐wildtype (n = 37) and IDH‐mutant glioma (n = 22). C Representative tissue cores (H&E, low‐power IHC, automated machine quantification, and high‐power IHC) reveal immunostaining ranging from 0.17 to 48.93. (Black = background [B], Blue = Tissue [T], Yellow “+” = staining cells). D , E Box plots of PTPN7 density by WHO grade for IDH‐wildtype or IDH‐mutant astrocytoma. F , G Comparisons of normal, low‐grade, and high‐grade groups. Elevated PTPN7 correlates with tumor grade in the IDH wildtype group but is obscure in the IDH mutant group

Article Snippet: Glioblastoma Visium dataset ( https://www.10xgenomics.com/datasets/human-glioblastoma-whole-transcriptome-analysis-1-standard-1-2-0 ).

Techniques: Immunohistochemical staining, Expressing, Mutagenesis, Immunostaining, Staining

Journal: Discover Oncology

Article Title: Dissecting PTPN7‐driven aggressiveness in IDH‐wildtype astrocytomas: multi‐omics, clinical validation, and spatial transcriptomics for prognostic insights

doi: 10.1007/s12672-025-02662-5

Figure Lengend Snippet: Spatial Distribution of PTPN7 in Glioblastoma and Its Correlation with Cell Fractions. A Box plot of PTPN7 expression (y-axis) across five histologic regions (x-axis): leading edge (n = 19), infiltrating border (n = 24), cellular tumor (n = 30), microvascular proliferation (n = 25), and pseudopalisading cells around necrosis (n = 24). The results showed that PTPN7 is significantly elevated in the cellular tumor zone (p = 0.046) versus the leading edge. B Correlation table summarizing Spearman coefficients (and p-values) for PTPN7 expression across various tumor, stromal, and immune cell subsets in each region

Article Snippet: Glioblastoma Visium dataset ( https://www.10xgenomics.com/datasets/human-glioblastoma-whole-transcriptome-analysis-1-standard-1-2-0 ).

Techniques: Expressing

Journal: Discover Oncology

Article Title: Dissecting PTPN7‐driven aggressiveness in IDH‐wildtype astrocytomas: multi‐omics, clinical validation, and spatial transcriptomics for prognostic insights

doi: 10.1007/s12672-025-02662-5

Figure Lengend Snippet: Spatial transcriptomic profiling of an adult glioblastoma via the 10 × Genomics Visium platform. A H&E image showing the tissue section. B A pseudocolor map of the PTPN7 expression is overlaid in the same section. Key tumor subregions—leading edge, infiltrating border, cellular tumor, peri‐necrotic area, and necrotic core—are delineated by dashed lines

Article Snippet: Glioblastoma Visium dataset ( https://www.10xgenomics.com/datasets/human-glioblastoma-whole-transcriptome-analysis-1-standard-1-2-0 ).

Techniques: Expressing

Journal: Discover Oncology

Article Title: Dissecting PTPN7‐driven aggressiveness in IDH‐wildtype astrocytomas: multi‐omics, clinical validation, and spatial transcriptomics for prognostic insights

doi: 10.1007/s12672-025-02662-5

Figure Lengend Snippet: Spatial transcriptomic profiling of an adult glioblastoma via the 10 × Genomics Visium platform. A H&E image showing the tissue section. B A pseudocolor map of the PTPN7 expression is overlaid in the same section. Key tumor subregions—leading edge, infiltrating border, cellular tumor, peri‐necrotic area, and necrotic core—are delineated by dashed lines

Article Snippet: To visualize PTPN7 expression in a spatial context, we examined a publicly available 10 × Genomics Visium dataset of an adult glioblastoma ( https://www.10xgenomics.com/datasets/human-glioblastoma-whole-transcriptome-analysis-1-standard-1-2-0 ).

Techniques: Expressing