Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Xenium]

ABSTRACT: Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Xenium]

PROVIDER: PRJNA1123296 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Xenium]

Project description:Spatial transcriptomics (ST) technologies enable the mapping of gene expression to specific regions within tissues. However, current ST platforms present inherent trade-offs between resolution and throughput, which cannot be entirely addressed by a single technology. To unravel the spatiotemporal landscape of gene expression and cellular interactions during kidney injury and repair, we employed an integrated approach combining Xenium's high-resolution in situ sequencing with Visium's whole-transcriptome spatial profiling.

2025-06-07 | GSE269719 | GEO

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair

Project description:Multimodal spatial transcriptomic characterization of mouse kidney injury and repair

| PRJNA1124059 | ENA

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

Project description:Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

| PRJNA1122779 | ENA

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

2025-06-07 | GSE269622 | GEO

Mouse Skin Xenium In Situ Spatial Gene Expression

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.

2024-12-11 | GSE276273 | GEO

Xenium Spatial Transcriptomics of Head and Neck Single Cell Carcinoma

Project description:Recent work has shown that the spatial organization of immune responses is a critical determinant of anti-tumor immunity. Here, we profiled ten head and neck squamous cell carcinoma (HNSCC) patient tumors and one ameloblastoma tumor using Xenium V1 spatial transcriptomics. The 10X genomics human multi-tissue and cancer gene expression panel targeting 377 genes was used in combination with 100 custom Xenium probes targeting patient-specific CDR3 regions of T cell receptors (TCRs) in T cells, additoinal T cell specific genes, HPV oncoprotein genes, and tumor genes of interest. This enabled the detection of 477 transcripts within each tumor sample at a single-cell resolution. For seven of the ten HNSCC samples, different tissue sections run on different days were analyzed as technical replicates. Together, these findings introduce a scalable platform for spatial clonal T cell analysis and provide new insight into the spatial relationship of cells within the HNSCC tumor microenvironment.

2025-08-06 | GSE300147 | GEO

Spatial transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [Xenium]

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.

2025-12-09 | GSE313006 | GEO

Entospletinib modulates spatial gene expression in kidney immune microenvironments during injury and repair

Project description:Spatial transcriptomic profiling was performed on mouse kidney sections using the NanoString GeoMx Digital Spatial Profiler with the Whole Transcriptome Atlas. Mice were subjected to ischemia-reperfusion injury (IRI) and treated with the SYK inhibitor Entospletinib or vehicle control. Regions of interest were selected from the renal cortex and medulla in two mice per condition at days 1, 7, and 14 post-injury. The dataset captures spatial gene expression dynamics during kidney injury and repair, and the effects of SYK inhibitio

2025-07-07 | GSE299516 | GEO

Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues - Xenium Data

Project description:Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmark the performance of three commercial iST platforms—10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx—on serial sections from tissue microarrays (TMAs) containing 17 tumor and 16 normal tissue types for both relative technical and biological performance. On matched genes, we find that Xenium consistently generates higher transcript counts per gene without sacrificing specificity. Xenium and CosMx measure RNA transcripts in concordance with orthogonal single-cell transcriptomics. All three platforms can perform spatially resolved cell typing with varying degrees of sub-clustering capabilities, with Xenium and CosMx finding slightly more clusters than MERSCOPE, albeit with different false discovery rates and cell segmentation error frequencies. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.

2025-10-03 | GSE308148 | GEO

Mouse Skin Xenium In Situ Spatial Gene Expression

Project description:Mouse Skin Xenium In Situ Spatial Gene Expression

| PRJNA1156206 | ENA