st data 10x genomics visium hd  (10X Genomics)

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: SCNT currently supports SC data generated from all major platforms, as well as ST data from 10X Genomics Visium and Visium HD.

Techniques: Expressing

Journal: PeerJ

Article Title: The burgeoning spatial multi-omics in human gastrointestinal cancers

doi: 10.7717/peerj.17860

Figure Lengend Snippet: The application of spatial profiling technologies in gastrointestinal cancer.

Article Snippet: Colorectal cancer , ST (10x Genomics Visium), in addition to scRNA-seq , Tumor specimens from four patients , 2022 ( ) .

Techniques: Sequencing, Next-Generation Sequencing, Multiplex Assay, Ligation, Amplification, Microarray, Mass Spectrometry, Imaging

Journal: Cell Reports Medicine

Article Title: scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network

doi: 10.1016/j.xcrm.2024.101568

Figure Lengend Snippet: Utilization of scRank for identifying neuronal subtypes targeted by fluoxetine in MDD (A) Top image displays snRNA-seq dataset of the dorsolateral prefrontal cortex (DLPFC) in Brodmann area 9 (BA9) derived from 17 patients with MDD. The lower image shows a schematic diagram of the mechanism of fluoxetine for MDD. scRNA-seq data for the MDD condition and the fluoxetine target gene were input data for scRank. (B) UMAP visualizations of data with 25 cell types colored based on the predicted rank for drug response. Bar plot shows the scaled perturbation score for each cell type. Ex, excitatory neurons; Inhib, inhibitory neurons; Oligos, oligodendrocytes; Endo, endothelial; Astro, astrocytes; OPC, oligodendrocyte precursor cells. (C) Heatmap of the GRN in excitatory neuron cluster 9 (Ex_9) with 205 MDD risk genes, which were separated into four modules. The top right heatmap represents the subnetwork of modules 2–4 for Ex_9, while the bottom right heatmap represents the network for inhibitory neuron cluster 5 (Inhib_5). Both heatmaps represent the GRN in untreated samples. The graphs to the right of the heatmap provide the network visualizations for module 2 in corresponding cell types, where gene nodes are colored based on their module. (D) Significantly enriched biological processes and pathways for module genes determined using the Metascape web tool. (E) Average module 2 activity for each neuron subtype in MDD. Data are presented as boxplots (minima, 25th percentile; median, 75th percentile; and maxima). The number of data points is 26 for each group. The comparison of the drug-target-related module for Ex_9 between the control group and MDD group is shown on the right, with respect to the averaged edge weight of 26 module 2 genes evaluated via a paired two-sided Wilcoxon test. (F) Averaged log fold change of MDD risk genes between healthy state and disease state. (G) Significantly activated pathways in Ex_9 determined via GSEA of the differentially expressed MDD risk genes. (H and I) Spatial mapping of Ex_9 using CellTrek. The images on the left in both (H) and (I) represent the layer annotation for each spatial spot in mouse anterior brain tissue (H) or human dorsolateral prefrontal cortex tissue (I). The images on the right in (H) and (I) represent the spatial distribution of Ex_9, where red pixels specifically mark the location of these neurons. The deeper layers (layers 5 and 6) are particularly highlighted. The subsequent bar plot shows the relative proportion of cells in each layer.

Article Snippet: For mouse brain ST data (10X Genomics Visium), we downloaded Seurat objects from ( https://satijalab.org/seurat/articles/spatial_vignette.html ).

Techniques: Derivative Assay, Inhibition, Activity Assay, Comparison, Control

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) Molecular cell type–based neuroanatomy of the goldfish telencephalon. Top: Color scheme shown above for GABAergic and glutamatergic cell types (dendrogram). Center: Eight coronal goldfish sections (goldfish 1), sampled for Visium ST, overlaid with a weighted color map that integrates all goldfish telencephalon cell types. Bottom: Regional parcellation based on color map differences above, each color indicates a different region, and suggested nomenclature annotated by similarity region names according to Northcutt . D , area dorsalis; V , area ventralis; Dc , large-celled subdivision of Dm ; Vsst , ventral Sst; Ppa , nucleus preopticus parvocellularis anterioris; a, anterior; p, posterior; d, dorsal; v, ventral; m, medial; l, lateral. ( B ) Heatmaps of SD (normalized per row) along lateral-medial (left) and dorsal-ventral (right) axes for top axial pattern genes, for goldfish 1 and 2; dots indicate spatial enrichment according to axial color scheme shown above; gray without dot, no enrichment. Right: Summary of axial score per gene (mean of enriched sections). ( C ) Expression of 14 axial-patterned genes across the goldfish telencephalon. Gray, low; red, high.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of GABAergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type assignment. Right: Expression of three branch-organizing genes. ( B ) All GABA types arranged in dendrogram order (GABA1 to GABA40), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cell type, visualized as pie charts. ( C ) Expression of three branch-organizing genes [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the GABAergic dendrogram for spatial correlation of Visium spots: five scRNA-seq cell types (columns) across eight a.-p. coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing, Marker, Gene Expression

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of glutamatergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type. ( B ) All glutamatergic types, in dendrogram order (GLUT1 to GLUT48), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cluster, visualized as pie charts. ( C ) Expression of two branch-organizing genes, NR2F2 and CNR1, visualized on t -SNE [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the glutamatergic dendrogram for spatial correlation of Visium spots: four scRNA-seq cell types (columns) across eight anterior-posterior coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Marker, Gene Expression, Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A and B ) t -SNE visualizing comparative species analysis between goldfish and zebrafish telencephalon, with cell types highlighted per species; (A) goldfish and (B) zebrafish. Per cell class, both species’ datasets are integrated (Harmony), followed by DBSCAN clustering. ( C ) Per cell type comparison, scored using KNN classifier. ( D ) Expression of CBLN1, PENK , and SST in the integrated teleostean dataset; dots (cells) colored by species origin. ( E ) Validation of gene expression detected in ST using HCR-FISH. Top row: Corresponding section overviews of genes detected in Visium (left) and HCR (right), where each spot represents a segmented fluorescent cell, colored by normalized expression. Bottom row: Raw fluorescent signal in zoom-ins, as indicated in overview sections.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Comparison, Expressing, Biomarker Discovery, Gene Expression