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: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.
Project description:Targeted spatial transcriptomic profiling was performed on seven formalin-fixed paraffin-embedded pleural mesothelioma tumor samples from four cases using the 10x Genomics Xenium platform. The Xenium Human Immuno-Oncology panel supplemented with 100 additional custom genes selected from known pleural mesothelioma biomarkers and single-cell RNA-seq-derived marker genes was used. Raw and processed Xenium files are provided for each sample. To ensure data integrity with downloaded Xenium files, md5 checksums are provided in 'Xenium_GEO.md5'. This dataset is part of a multi-modality study including matched scRNA-seq, bulk RNA-seq, and Xenium spatial transcriptomics generated from overlapping pleural mesothelioma samples. Related controlled-access sequencing data are available in dbGaP under accession phs004285.
Project description:Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed Xenium in situ analysis in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.
Project description:One of the most common origins of Peritoneal metastasis (PM) is colon cancer, which occurs in about 20% of colon cancer patients. Given the cancer cell heterogeneity in PM, we first tried to dissect the spatial distribution of CAF and the associated niches at a single cell resolution, we exploited the Xenium In Situ high-plex spatial imaging platform. We performed the Xenium assays with 8 human PM samples of colon origin including one PM-adjacent tissue. Among the 8 PM samples, 3 samples carried a distinct iCMS3 epithelial signature (PM1, PM2, PM3), 2 carried iCMS2 signature (PM6, PM7), while the other 2 samples had a mix of both iCMS2 and iCMS3 signatures (PM4, PM5). We found that the presence of iCMS3 cancer cells was associated with an increase infiltration of lymphocytes and the formation of tertiary lymphoid structures (TLS).