Project description:To investigate the effecs of commensal papillomavirus immunity on the homeostasis of highly mutated normal skin, spatial transcriptomics (Xenium, 10x Genomics, Pleasanton, CA) was performed on SKH-1 mouse back skin. The mice were treated with mouse papillomavirus (MmuPV1) or virus-like particles (VLP), followed by UV exposure for 25 weeks.
Project description:Treatment of mouse skin with the staphylococcal protease SspA and house dust mite extract (HDM) results in dermatitis. Using a 10x Genomics Xenium In Situ platform, we analyzed spatial features in mock-treated skin and inflamed skin treated with epicutaneous SspA and HDM.
Project description:Wound-edge skin section of patients with low or high-biofilm infections defined based on the biofilmQ analysis were evaluated using Xenium spatial transcriptomes custom 470-gene expression panel that included built-in human-, mouse-, and bacteria-specific probes, as well as positive and negative controls.
Project description:Xenium-based spatial transcriptomics was performed to characterize cellular heterogeneity and spatial organization in muscle-invasive bladder cancer (MIBC). Xenium enabled high-resolution in situ mapping of selected gene expression at single-cell resolution in formalin-fixed paraffin-embedded (FFPE) tissue sections. Together, these data provide complementary insights into tumor cell states, lineage programs, and their spatial relationships with the tumor microenvironment, including immune and stromal components. This dataset enables investigation of tumor heterogeneity, lineage plasticity, and spatially resolved cell–cell interactions in MIBC.
Project description:We generate Visium 10x data from healthy skin (n=2) and inflamed atopic dermatitis skin (n=1). We generate Xenium 10x data from non-lesional atopic dermatitis skin (n=2) and inflamed atopic dermatitis skin (n=1). We use these datasets to locate skin fibroblast subtypes identified from scRNA-seq.
Project description:To spatially contextualize and extend disease-associated cellular states, we generated Xenium spatial transcriptomics data from FFPE lung tissue of 38 participants spanning the COPD disease spectrum. Four tissue microarrays (TMA1–TMA4) were profiled using a custom 480-gene Xenium panel. These data capture the in situ organization of inflammatory, regenerative, and remodeling cell states and reveal spatially localized niches and patterns of cell–cell communications relevant to COPD pathology. This dataset provides high-resolution spatial context for characterizing microenvironmental structure and cell–cell interactions in COPD lung tissue.
Project description:Lactate transport is an important regulator of cellular metabolism and may contribute to fibroblast activation and extracellular matrix remodeling during pulmonary fibrosis. To define the spatial transcriptional landscape associated with pharmacologic inhibition of lactate transport during fibrotic lung remodeling, we performed spatial transcriptomic profiling of mouse lung tissue using the 10x Genomics Xenium Analyzer. Lung sections from mice with bleomycin-induced pulmonary fibrosis treated with inhibitors of monocarboxylate transport were analyzed using the Xenium Prime 5K Mouse Pan Tissue & Pathways panel to generate cell-resolved spatial gene expression maps. The resulting dataset provides spatially resolved transcriptional profiles across epithelial, stromal, endothelial, and immune compartments of the injured lung, enabling analysis of fibroblast activation states and spatial microenvironments associated with fibrotic remodeling.
Project description:We developed a method that utilizes floating mounting of thin sections of fixed frozen mouse lung tissue onto Xenium slides for the fluorescent in situ hybridization (FISH) and imaging–based spatial transcriptomics analysis of gene expression using the Xenium platform provided by 10X Genomics. Spatial transcriptomics techniques provide a comprehensive view by merging gene expression data with spatial context within their native tissue architecture. However, the Xenium pipeline has been validated only for formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections by 10X Genomics. Notably, many researchers prefer paraformaldehyde-fixed cryosections for immunohistochemistry and in situ hybridization. In our study, we assessed the compatibility of standard fixed frozen mouse lung sections with the Xenium protocol. Our findings reveal that these sections not only align well with the Xenium platform but also offer superb imaging and gene expression quantification, even with limited number of genes in the Xenium panel. This protocol can serve as a valuable resource for preparing various tissues where FFPE and fresh frozen samples present challenges.