Project description:This dataset provides single-nucleus RNA-sequencing (snRNA-seq) profiles of wild-type mouse spleen, generated as a matched, transcriptome-wide reference for the SpatialBench resource benchmarking high-resolution spatial transcriptomics platforms (Visium HD, Xenium and MERSCOPE). Spleens were collected from C57BL/6J mice infected intravenously with Plasmodium berghei ANKA to induce splenic germinal-center formation, then drug-cured with chloroquine and pyrimethamine, and processed into formalin-fixed paraffin-embedded (FFPE) blocks. Nuclei were isolated from FFPE scrolls by pestle dissociation (10x Genomics CG000632) and profiled with the probe-based 10x Genomics Chromium Fixed RNA Profiling (Flex) singleplexed assay (CG000691), targeting ~10,000 nuclei per sample. These nuclear profiles were used for cell-type annotation and gene-level concordance benchmarking against the matched spatial datasets.
Project description:To test whether sex and diet influence cell-type specific gene expression in the mouse liver, we performed Visium HD spatial transcriptomics on liver tissue from male and female mice fed standard or Western diet.
Project description:We investigated the single-cell spatial transcriptomics of murine normal pancreas (N), pancreatitis (P) and PDAC formalin-fixed paraffin-embedded (FFPE) samples using Visium HD.
Project description:We have now developed an organoid-based model of gastric cancer from GAstric Neoplasia (GAN) mice, which express Wnt1 and the enzymes COX2 and microsomal prostaglandin E synthase 1 in the stomach. Both p53 knockout (GAN-p53KO) organoids and KRASG12V-expressing GAN-p53KO (GAN-KP) organoids were generated by genetic manipulation of GAN mouse–derived tumor (GAN-WT) organoids. To uncover the molecular mechanism underlying the intratumoral heterogeneity of GAN-KP tumors, we performed spatial transcriptomics analysis with the 10× Genomics Visium platform, which allows characterization of the spatial topography of gene expression.
Project description:To characterize the tumor microenvironment and elucidate mechanisms of immune evasion in malignant adrenal tumors, we performed spatial transcriptomics (Visium HD) on pathological specimens from adrenocortical adenoma (ACA) and pheochromocytoma mixed tumor. Using each cell’s spatial coordinates and gene expression profiles, we inferred tumor cell–immune cell interactions.
Project description:This submission contains raw 10x Genomics Visium HD Spatial Gene Expression FASTQ files from three FFPE mucosa-associated lymphoid tissue lymphoma samples analyzed in the O2 marginal zone lymphoma study. Processed Space Ranger and downstream spatial transcriptomics files will be added before final GEO release. Submitter contact email: lcxujiadai@163.com.
Project description:The spatial transcriptomic analysis of barley embryos in response to 75 µM ABA was investigated using Visium Spatial Transcriptomics (10×Genomics) technology. Embryo sections were collected from wild-type 'Sebastian' and a double mutant hvcbp20.ab/hvcbp80.b impaired in both subunits of the Cap-Binding Complex (CBC): CBP20 and CBP80 at 1 day after imbibition (DAI) under control and 75 µM ABA conditions. Cryosectioned tissues were stained, mounted on Visium slides, and processed for spatial gene expression profiling. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 151 bp). The data were aligned to the barley reference genome (cv. MorexV3) and used to identify differentially expressed genes (DEGs) across six distinguished embryonic regions: coleoptile, cotyledon, mesocotyl, plumule, scutellum, and radicle. The dataset provides insights into the spatial regulation of ABA-responsive genes in embryos during barley seed germination.
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:Using Visium HD spatial transcriptomics and immunostaining, we mapped skin compartment dynamics during DPCP-induced allergic contact dermatitis. Dermal white adipose tissue transitioned from metabolic homeostasis to immune activation and inflammatory remodeling, accompanied by sustained lipolysis. Concurrently, CD45⁺ immune cells accumulated in the lower dermis and dWAT. These findings identify dWAT as an immune-metabolic hub orchestrating inflammatory progression and highlight spatial transcriptomics as a powerful tool for dissecting skin niche regulation.
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.
