Project description:Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization. Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos.
Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".
Project description:Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 (HHV-7) infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In this dataset spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in “immune-hot” cases and immune foci even in otherwise “cold” cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.
Project description:To investigate spatial heterogeneities in the axolotl forebrain, a coronal section of it was obtained for spatial transcriptomics using Visium V1.
Project description:To reveal the spatial distribution and the difference gene expression pattern of cancer cells in colorectal cancer, Visium spatial transcriptomics of four CRC patients was applied
Project description:Identification of cell types in the interphase between muscle and tendon by Visium Spatial Transcriptomics of four human semitendinous muscle-tendon biopsies. Cell types identified by single nuclei RNA seq on similar tissue were localized in situ with the use of Spatial Transcriptomics.
Project description:Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging.
Project description:Neutrophils are increasingly recognized as key players in the tumour immune response, and are associated with poor clinical outcomes. Multiple studies have characterised various neutrophil states within the tumor, with associated pro- and anti- tumoral functions. However, it is unknown if this heterogeneity of neutrophils is contributed by their surrounding tumor microenivironment. To answer this, we performed 10X Visium spatial transcriptomics on a murine model of pancreatic cancer. We discovered that terminally differentiated T3 neutrophils localise primarily in regions near hypoxic and glycolytic areas, while transitional immature T1 and mature T2 neutrophils localise towards the peripheral regions of the tumors. This results points to a spatially dependent role of T3 neutrophils, which may be critical to carry out pro-tumorigenic functions.