Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tumor-stromal crosstalk and macrophage enrichment is associated with chemotherapy response in bladder cancer

ABSTRACT: This dataset provides a spatial transcriptomic atlas of bladder cancer tissue treated ex vivo with standard chemotherapy. Tumor specimens from eight bladder cancer patients were excised and treated for 48 hours with gemcitabine and cisplatin (GemCis) or medium control (MSC), followed by formalin fixation and paraffin embedding. Spatial gene expression profiling was performed using the NanoString GeoMx Digital Spatial Profiler Whole Transcriptome Atlas (WTA), capturing expression of over 18,000 transcripts. Tumor regions were identified by cytokeratin (CK) staining and analyzed alongside adjacent stroma (CK-negative). Chemotherapy treatment led to significant transcriptomic alterations, including downregulation of pathways related to substance uptake (e.g., endocytosis) and metabolism (e.g., glycolysis), and upregulation of cell death pathways. Cellular deconvolution using xCell revealed stromal M2 macrophage enrichment in chemotherapy-resistant samples, suggesting a microenvironmental contribution to resistance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE296955 | GEO | 2025/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE296955_ProcessedDataGemCis.xlsx	Xlsx

Items per page:

1 - 2 of 2

Similar Datasets

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human cell pellet array]

Project description:Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ∼10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.

2022-03-01 | GSE186714 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

2022-03-01 | GSE190088 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]

2022-03-01 | GSE186594 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

2022-03-01 | GSE188451 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse organ array]

2022-03-01 | GSE187013 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse cell pellet array]

2022-03-01 | GSE187000 | GEO

BCG vaccination stimulates Integrated Organ Immunity by feedback of the adaptive immune response to imprint prolonged innate antiviral resistance [GeoMx]

Project description:GeoMx Whole Transcriptome Atlas (WTA) of mouse lungs with CD4, PanCK, DAPI staining

2023-12-04 | GSE247145 | GEO

Comprehensive Atlas of the Mouse Urinary Bladder

Project description:We report the application of single-cell based sequencing for high throughput profiling of the mouse urinary bladder. By utilizing multiple dissociation techniques and library preparation techniques we generated an atlas comprising 43,119 cells including major cell types absent from previous reports. We found that previous single-cell profiling of the mouse bladder lacked a major cell type in the detrusor smooth muscle and incorrectly annotated other cell types such as mesothelial cells. Using the atlas, we elucidated aspects of bladder biology including urothelial differentiation, the identity of interstitial cells of Cajal, detrusor smooth muscle control and immune distributions. Finally, we combine the single-cell based sequencing with spatial transcriptomics and imaging mass cytometry to add spatial context to transcriptomic profiling.

2021-12-21 | GSE180128 | GEO

GeoMx digital spatial profiling on biopsies of triple negative breast cancer patients

Project description:In this study, we analyzed the differential spatial transcriptome of Triple-Negative Breast Cancer (TNBC) patients who responded in an opposite manner to neoadjuvant chemotherapy (NACT): we compared responders displaying pathological complete response (pCR) with no-responders who showed disease progression during therapy. Diagnostic TruCut biopsies were analyzed using the GeoMx Cancer Transcriptome Atlas (Nanostring).

2023-10-12 | E-MTAB-13069 | biostudies-arrayexpress

Spatial transcriptomic profiling of FFPE and frozen colorectal cancer tissues

Project description:This dataset contains spatial whole-transcriptome profiles from colorectal cancer (CRC) tissues preserved using formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF) methods. Samples were obtained from a patient with stage IV CRC during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Each tissue type was sectioned, stained for Pan-cytokeratin (PanCK), CD45, and SYTO13, and analyzed using the NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas panel. A total of 36 areas of illumination (AOIs) representing epithelial (PanCK⁺), immune (CD45⁺), and stromal (PanCK⁻/CD45⁻) compartments were collected. Sequencing was performed on an Illumina NovaSeq 6000 platform, and raw counts were processed using NanoString DSP Analysis Suite v3.1 and R for normalization and quality control. This dataset provides spatially resolved gene-expression information across different preservation conditions of CRC tissues to support comparative analysis and method evaluation in spatial transcriptomics.

2025-11-17 | GSE310215 | GEO