visium spatial tissue optimization slide reagent kit  (10X Genomics)

Journal: JCI Insight

Article Title: A potent inhibitor of PAI-1, MDI-2517, mitigates disease severity in a preclinical systemic sclerosis model

doi: 10.1172/jci.insight.195005

Figure Lengend Snippet: ( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on the 10x Visium spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .

Article Snippet: Optimization of tissue permeabilization was performed on 20 μm sections using a Visium Spatial Tissue Optimization Reagents Kit (10x Genomics), which established an optimal permeabilization time of 9 minutes.

Techniques: Comparison, Expressing, Control, Modification, Marker, Single Cell, RNA Sequencing, MANN-WHITNEY

Journal: bioRxiv

Article Title: Brassinosteroids mediate proper coordination of sepal elongation

doi: 10.1101/2025.07.13.664398

Figure Lengend Snippet: Spatial RNAseq further suggests boundary identity, cytokinin signaling, and brassinosteroid signaling are increased in drmy1 . A) Cartoon of a typical transverse section of an ap1cal 35S::AP1-GR cauliflower-like cluster, showing the developing flower buds with initiating sepals on the outer ring . B) Representative brightfield images of transverse sections of WT and drmy1 in the ap1cal 35S::AP1-GR background. n=9 Total WT replicate cauliflower-like clusters, n=22 drmy1 replicate cauliflower-like clusters (See also Figure S3). C) An overlay of which single cell cluster maps with the highest prediction score to each Visium spot on the same tissue shown in panel (B). See figure S3 for a more detailed view of prediction scores from each single cell cluster. D) The proportions of Visium spots grouped by which single cell cluster mapped to each with the highest prediction score (clusters that mapped to <10 spots in either genotype were omitted). For cluster 2 (boundaries), WT = 0.102, drmy1 = 0.232. E-G) Overlays of the percentage of transcripts from cytokinin downregulated genes (E), brassinosteroid downregulated genes (F), and SCT normalized expression of DWF1 , a brassinosteroid biosynthesis gene (G). H) Dotplot showing the differences in expression of genes up and down-regulated by various hormones. For each cell, the percentage of transcripts that come from the set of genes up or downregulated by applications of these hormones according to is calculated, then the mean of all the cells in each cluster is calculated for WT and drmy1 . The size of each dot represents the log of the inverse of the p-value between the mean of the two genotypes with a Bonferroni adjusted threshold of p < 0.00069. The color of each dot represents the percentage increase or decrease of the mean of drmy1 compared to WT. Scale bars 500 μm See also: Figure S3, S4

Article Snippet: To optimize RNA permeabilization, we used the Visium Spatial Tissue Optimization Slide & Reagent Kit, 4 slides (10x Genomics PN-1000193).

Techniques: Expressing

Journal: bioRxiv

Article Title: Spatial and single-cell transcriptomics capture two distinct cell states in plant immunity

doi: 10.1101/2025.06.03.657683

Figure Lengend Snippet: A) Schematic of experiments performed for various samples of ASR-infected soybean leaf. Leaves infected for 4 days were paradermal (PD) and cross sectioned (CS), leaves infected for 7 days were cross sectioned for Visium spatial analysis. Leaves infected for 1, 3, and 5 days were subjected to snRNA-seq. B) Percent ASR reads per spot mapped spatially reveals localized regions of ASR infection. C) Spatial UMAP of percent ASR reads per spot. D) snRNA-seq UMAP of percent ASR reads per nuclei.

Article Snippet: Reverse-transcription and tissue removal were performed using reagents from the Visium Spatial Tissue Optimization Reagent kits (10x Genomics #PN-1000193).

Techniques: Infection