genomics visium hd assay  (10X Genomics)

Journal: Cell Reports Methods

Article Title: Differential expression analysis in single-cell and spatial RNA-seq without model assumptions

doi: 10.1016/j.crmeth.2026.101383

Figure Lengend Snippet: Weighted statistical testing reduces false-positive DGE in spRNA-seq (Visium HD assay) (A) Top: Proliferating chondrocytes were selected in 3 sections from the same E18.5 tibia; shaded areas show the selected regions in high resolution images of H&E-stained sections. Bottom: Zoomed images of the selected areas. Colored dots mark 8 × 8 μm 2 bins used for the analysis of gene expression, which passed quality control based on the following criteria: >20 features per bin, >100 counts other than Col1a1 or Col1a2 per bin, mitochondrial genes between 0.1% and 5% UMI, and Col2a1 > 5% UMI. The bin color represents the relative expression of Col2a1 ( n Col 2 a 1, i ×10,000). (B) DGE analysis performed with the weighted t test- χ 2 test combination and Seurat’s FindMarkers function for all 3 possible pairwise comparisons between the selected areas. Only genes detected in at least 10% of the bins were analyzed.

Article Snippet: For simplicity and consistency, we compare the results produced by our method with the standard models within the Seurat workflow, using publicly available 10× Genomics scRNA-seq datasets ( https://www.10xgenomics.com/datasets ) and our spRNA-seq data collected with the 10× Genomics Visium HD assay.

Techniques: HD Assay, Staining, Gene Expression, Control, Expressing

Journal: medRxiv

Article Title: Development and first-in-human CAR T therapy against the pathognomonic MiT-fusion driven protein GPNMB

doi: 10.1101/2025.02.26.24319604

Figure Lengend Snippet: a , Hematoxylin and eosin (H&E; left panel) of lung tumour biopsy sample taken 35 days post-GCAR1 treatment, with (remaining panels) IHC staining for the CAR target GPNMB; TFE3 to mark tumor cells; CD3 to identify all T cells; MYC to identify GCAR1 cells. Scale bars = 100 μm. b , Spatial plot of GPNMB gene expression across three samples profiled with Visium HD, including the ASPS-3 patient primary tumor and 2 research core biopsies. c , H&E plots of the spatially profiled samples in (b), with spatial plots of gene expression program usage values, and top 10 scoring genes per program (heatmaps). d , Barplots of the proportion of 24 μm bins per sample that have a minimum usage of each program (usage >0.05). Primary (grey); biopsy (green). Biopsy samples are merged together. e , Pearson correlation between spatial GPNMB expression in each sample type (rows) and spatial program usage (columns). f , Heatmap plot of the inverse rank of selected genes (rows) in each program (columns). Values indicate the relative importance of these genes to defining a given program. g , Pearson correlation of gene expression (rows) and program usage (columns) values in the biopsy samples. Checkpoint receptor genes with high correlation to Program 9 (CD8 T cells) are boxed in black; ligands are boxed in red when involving tumor or vascular programs. h , Dot plot of T cell program co-usage within T cell spatial niches in the biopsy samples. Niches are T cell positive bins stratified based on the additional presence of fibroblasts (niche 1), pericytes and endothelial cells (niche 2), or the absence of those stromal components (niche 3; i.e. tumor). Within each T cell niche, program co-usage is calculated for each of 15 programs, setting bins with usage to 1, otherwise 0. The proportion of 1 vs 0 bins are summarized for each niche. i , Schematic of the strategy for T cell-proximal gene expression analysis performed in panel (j). Each 24 μm bin positive for a T cell (based on expression of any T cell gene, including (CD3 components, CD4, CD8A, or GCAR) was considered to be within the region of interest, while the remaining bins were considered outside. The radius around each T cell was increased by 1, to encompass up to 3 nearest neighbours. j , Proportion of bins within and outside T cell regions in each sample (primary tumor, biopsy cores, xenograft), positive for expression of PD1 (top row) and PDL1 (bottom row). k, Heatmap of Student’s t-test (two-sided) p-values among pairs of regions (n=4 values per region) from panel (j).

Article Snippet: The Visium HD Spatial Gene Expression Kit (10x Genomics, human probe panel) was used to profile two ASPS biopsy samples, one region of the primary tumor, and a xenograft sample.

Techniques: Immunohistochemistry, Gene Expression, Expressing

Journal: bioRxiv

Article Title: Defining the cell and molecular origins of the primate ovarian reserve

doi: 10.1101/2025.01.21.634052

Figure Lengend Snippet: B) Spatial distribution of genes of interest in Visium CytAssist analysis of W5 and W6 ovaries mapped onto a black and white H&E image. Ovary (white), mesonephros (orange) and adrenal (yellow) regions are outlined; expression level scaled from blue (min) to yellow (max). (C) CosMx spatial molecular imager (SMI) analysis of W6_3 ovaries; left panels, distribution of annotated cell clusters in the selected fields of view (FOVs); right panels, zoom in on ovary region with cell segmentation overlay showing germline, pre-granulosa and stromal cells (additional clusters marked “Others”). White dashed line indicates ovary region. (D) Immunofluorescence analysis for known genes (WT1, blue; GATA4, orange; FOXL2, yellow; VASA, green; NR2F2, magenta) and genes identified in the DEG analysis (NR5A1, red; GATM, cyan) in W5 and W6 ovaries. Scale bars 50 µM.

Article Snippet: To do this, we performed spatial transcriptomics on W19_3, using the 10x Genomics Visium HD CytAssist platform with the human whole transcriptome probe set, and used the clusters identified in our 10x Chromium analysis to assign cell type identity to given bins ( ; see Methods).

Techniques: Expressing, Immunofluorescence

Journal: bioRxiv

Article Title: Defining the cell and molecular origins of the primate ovarian reserve

doi: 10.1101/2025.01.21.634052

Figure Lengend Snippet: (A) UMAP plot of single cells collected from rhesus fetal ovaries at W8, W15 and W19 colored according to Seurat clusters (n=3 biological replicates per timepoint). (B) Bar graph of annotated cell type proportions at each time point. (C ) UMAP plot of W8 cells colored by cell annotation from the analysis in . (D) Expression of ovary-enriched genes identified in the Visium CytAssist spatial transcriptomics analysis at W5 and W6 cast on the UMAP plot from . Normalized expression plotted on a high-to-low scale (indigo-yellow). (E) UMAP plot of granulosa subset (clusters a1, a3 and a4 from 3A) re-clustered and colored according to Seurat clusters . (F) Bar graph of granulosa sub-cluster proportions at each time point. (G) Dot plot of known granulosa-associated genes, or genes identified as highly enriched in each cluster (rectangles). Expression plotted on a high-to-low scale (indigo-yellow); dot size reflects percentage of cells expressing given gene. *KRT18 = ENSMMUG00000031911 ), * COL9A3 = ENSMMUG00000016859 .

Article Snippet: To do this, we performed spatial transcriptomics on W19_3, using the 10x Genomics Visium HD CytAssist platform with the human whole transcriptome probe set, and used the clusters identified in our 10x Chromium analysis to assign cell type identity to given bins ( ; see Methods).

Techniques: Expressing

Journal: bioRxiv

Article Title: Defining the cell and molecular origins of the primate ovarian reserve

doi: 10.1101/2025.01.21.634052

Figure Lengend Snippet: (A) VASA (green), NR2F2 (magenta), FOXL2 (yellow), NR5A1 (red), GATM (cyan) expression and DAPI (grey) at W8, W15 and W19. Scale bars 50 µM. (B) VASA (yellow), KRT19 (cyan), FOXL2 (magenta), expression and DAPI (grey) in primordial follicles at W19. Scale bars 50 µM. (C) Spatial distribution of germline bins (E) and granulosa PG1 subcluster bins identified in Visium CytAssist HD analysis of W19_3 mapped onto a black and white H&E image. See Methods for details.

Article Snippet: To do this, we performed spatial transcriptomics on W19_3, using the 10x Genomics Visium HD CytAssist platform with the human whole transcriptome probe set, and used the clusters identified in our 10x Chromium analysis to assign cell type identity to given bins ( ; see Methods).

Techniques: Expressing

Journal: bioRxiv

Article Title: Defining the cell and molecular origins of the primate ovarian reserve

doi: 10.1101/2025.01.21.634052

Figure Lengend Snippet: (A) Visium CytAssist HD spatial distribution of granulosa cluster g9 and theca clusters t0 and t2 bins identified in W19_3 mapped onto a black and white H&E image. (B) VASA (green), CYP17A1 (yellow) expression and DAPI (grey) at W19 and 6 MPN. (C) NR5A1 (yellow), FOXL2 (magenta), PAPP-A (red), CYP19A1 (cyan) expression and DAPI (grey) in fetal activated follicles at W19. Magnified area (dashed) is shown in the inset. ( D ) VASA (green), CYP17A1 (yellow), FOXL2 (magenta), WT1 (blue) expression and DAPI (grey) at W19 and 6MPN. Magnified area (dashed) is shown in the inset. All scale bars 50 µM.

Article Snippet: To do this, we performed spatial transcriptomics on W19_3, using the 10x Genomics Visium HD CytAssist platform with the human whole transcriptome probe set, and used the clusters identified in our 10x Chromium analysis to assign cell type identity to given bins ( ; see Methods).

Techniques: Expressing