Journal: STAR Protocols

Article Title: Protocol to evaluate mouse brain spatial cell type-resolved transcriptomic discoveries using 10× Visium spatial transcriptomics and FLEX scRNA-seq

doi: 10.1016/j.xpro.2025.104277

Figure Lengend Snippet: Web summary metrics generated from 10× Genomics SpaceRanger Web summaries generated from 10× Genomics Space Ranger pipeline after receiving raw data for P0 mouse tissue in Visium spatial transcriptomics step. The summary page will provide detailed information regarding data quality including “Fraction Reads in Spots Under Tissue”. To determine localization of diffused RNA and confirm that RNA is “leaking” from tissue section, rerun Space Ranger on all spots in the Visium capture area. If Fraction Reads in Spots Under Tissue is below 50%, optimization is required. (A) Unsuccessful reads in spots are most likely due to over permeabilization when releasing RNA. (B) Successful processing of P0 tissue with 10× Visium.

Article Snippet: Permeabilization time is determined with Visium Spatial Tissue Optimization (protocol CG000238) which needs to be performed before starting Spatial Transcriptomics Tissue Processing.

Techniques: Generated

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