Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human bladder cell spatial mapping [Xenium]

ABSTRACT: We used Xenium In Situ assay with a custom probe panel to visualize a human bladder cross-section. The custom probe panel contains probe sets against bladder cell type marker genes and RNA isoforms to enable cell identification. We detected 30 distinct cell groups consisted of urothelial cell states, immune cells, and various stromal cell types.

ORGANISM(S): Homo sapiens

PROVIDER: GSE345644 | GEO | 2026/09/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Human bladder cell spatial mapping

Project description:We used Xenium In Situ assay with a custom probe panel to visualize a human bladder cross-section. The custom probe panel contains probe sets against bladder cell type marker genes and RNA isoforms to enable cell identification. We detected 33 distinct cell groups consisted of urothelial cell states, immune cells, and various stromal cell types.

2025-12-19 | GSE297459 | GEO

High resolution mapping of human skin chronic wound tissues biofilm infected using integrated single-cell, spatial and in situ analysis [Xenium]

Project description:Wound-edge skin section of patients with low or high-biofilm infections defined based on the biofilmQ analysis were evaluated using Xenium spatial transcriptomes custom 470-gene expression panel that included built-in human-, mouse-, and bacteria-specific probes, as well as positive and negative controls.

2026-08-05 | GSE313808 | GEO

Targeted spatial transcriptomic profiling of pleural mesothelioma using 10x Genomics Xenium

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.

2026-04-08 | GSE327347 | 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

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 analysis of human dorsoal root ganglia neurons [Xenium]

Project description:Xenium platform was used for the spatial transcriptomic analysis of human DRG neurons, 100 marker genes were selected as the customized probe panel and hybridized to fresh frozen hDRG sections. Manual segmentation of each neuron soma was performed, based on expressions of pan-neuronal marker gene PGP9.5, satellite glia cell marker FAB7B, and the corresponding H.E. staining. In total, 1340 neurons were identified (excluding 75 region-of-interest with poor or unclear neuronal soma morphology in H & E staining) and clustered into 16 groups. The 16 clusters were assigned as different cell types based on marker genes expression.

2024-08-14 | GSE273557 | GEO

Spatial atlas of the human brain vasculature reveals specialized cell ensembles

Project description:10x Genomics Xenium profiling of human temporal cortex and hippocampus with custom cerebrovascular-focused gene panel

2026-07-31 | GSE335898 | GEO

A Xenium Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities

Project description:Xenium-based spatial transcriptomics was performed to characterize cellular heterogeneity and spatial organization in muscle-invasive bladder cancer (MIBC). Xenium enabled high-resolution in situ mapping of selected gene expression at single-cell resolution in formalin-fixed paraffin-embedded (FFPE) tissue sections. Together, these data provide complementary insights into tumor cell states, lineage programs, and their spatial relationships with the tumor microenvironment, including immune and stromal components. This dataset enables investigation of tumor heterogeneity, lineage plasticity, and spatially resolved cell–cell interactions in MIBC.

2026-05-05 | GSE326226 | GEO

Spatial Transcriptomic Analysis of a Human Bone Marrow Clot Biopsy Using Xenium 5K

Project description:A normal human bone marrow clot biopsy was analyzed using the Xenium 5K panel and annotated with BinarySPA.

2026-04-10 | GSE322974 | GEO

Homo sapiens

Project description:Human PBMC RNA Expression, Nanostring custom probe panel

| PRJNA508089 | ENA