Project description:Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This submission contains the Space Ranger processed outputs from Visium spatial transcriptomic sequencing (10x Genomics), including paired high-resolution H&E tissue images. We also provide an integrated single cell and spatial dataset across 97 Visium sections, including gene expression, cell state abundances, and histopathological annotations.
Project description:Human uterine samples were analysed using Visium technology (10X Genomics) to generate a cellular 2D map of the endometrium to study its temporal and spatial changes across the menstrual cycle. Dataset comprises 4 samples from two women in their reproductive age.
Project description:One healthy mouse brain and one glioblastoma tumor derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium HD Spatial Gene Expression chemistry.
Project description:Two primary and two post-radiotherapy recurrent glioblastoma tumors derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium Spatial Gene Expression v1 chemistry.
Project description:Spatial transcriptomics facilitates the understanding of gene expression within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics’ Visium which provides whole tissue section profiling, enabling whole transcriptome spatial analysis. Our dataset comprises spleen tissue from mice infected with malaria, spanning multiple experiments and sample preparation protocols for tissue preservation, either as fresh frozen at optimal cutting temperature (OCT) or formalin-fixed paraffin-embedded (FFPE). Tissue placement was also considered, comparing direct tissue placement on the slide with the use of CytAssist (CA), which expands the Visium platform’s capabilities by allowing for the pre-selection of tissue sections and genes through a set of probes. We also include a matching scRNA-seq dataset that can be integrated with the spatial data.
Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).
Project description:We applied spatial transcriptomic profiling (10x Genomics Visium) to meningioma samples across grades and methylation classes, in order to characterize features of meningioma heterogeneity across subgroups. We identified an overall decrease in myeloid cell proportions from grade 1 to grade 3 meningiomas, as well as a phenotypic shift from microglia-like cells towards a myeloid-derived proliferative macrophage phenotype.
Project description:We report a bulk transcriptomic dataset of mouse dorsal hippocampus to identify gene expression changes of spatial object recognition training. We report a spatial transcriptomics dataset of mouse brain tissue generated with the 10x Genomics Visium platform to identify gene expression profiles of spatial object recognition training. We report a single nuclei ATAC-seq and a Single nuclei RNA-sequencing using SPLiT-pool barcoding datasets of mouse dorsal hippocampus to identify chromatin and gene expression changes of spatial object recognition training.
Project description:To study the spatial localisations of the cell populations in an early haematopoietic tissue and lymphoid organs critical for T and B cell development, we profiled fetal liver, thymus and spleen from 3 donors at 18 PCW with sequencing-based spatial transcriptomics (10x Genomics Visium).