Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptome profiling for nasopharyngeal carcinoma [GeoMx-DSP]

ABSTRACT: Spatial transcriptome profiling for nasopharyngeal carcinoma [GeoMx-DSP]

PROVIDER: PRJNA1276487 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic profiling of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

Project description:To study how targeting CMTM6 inCRCs influences the transcritome. Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

2025-06-11 | GSE253937 | GEO

Transcriptomic profiling of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

Project description:To study how targeting Glut1 in CAFs influences the transcritome of adjacent cancer cells, MC38 adjacent to control CAFs and Glut1-deficient CAFs were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

2024-02-18 | GSE225457 | GEO

Transcriptomic profiling of Adjacents CAFs of MC38 tumor cells on murine MC38 liver metastasis sections by NanoString GeoMX DSP

Project description:To study how targeting CMTM6 in CRCs influences the transcritome. Adjacents CAFs of Control MC38 and CMTM6-deficient MC38 were subjected to spatial transcriptomic profiling with the NanoString GeoMx DSP

2025-06-11 | GSE253938 | GEO

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)

Project description:We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

2024-11-01 | E-MTAB-14566 | biostudies-arrayexpress

GeoMX spatial transcriptomic on biphasic Malignant Pleural Mesothelioma

Project description:We applied a spatially resolved, high-dimensional transcriptomic approach to study MPM morpho-logical evolution. 139 regions across 8 biphasic MPMs (B-MPMs) were profiled using the GeoMx™Digital Spatial Profiler and Cancer Transcriptome Atlas to compare epithelioid and sarcomatoid components transcriptional profile and reconstruct the positional context of transcriptional activities and the spatial topology of MPM cells interactions.

2023-12-07 | E-MTAB-13043 | biostudies-arrayexpress

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (Chromium and Visium)

2024-11-01 | E-MTAB-14560 | biostudies-arrayexpress

Transcriptomic profiling of the cancer-associated fibroblasts (CAFs) on murine MC38 liver metastasis sections by NanoString GeoMX DSP

Project description:To study how targeting Glut1 influences the transcriptome of cancer-associated fibroblasts (CAFs), the transcriptome of control CAFs and that of Glut1-deficient CAFs on murine MC38 liver metastasis sections were obtained and compared with the NanoString GeoMx DSP

2024-02-18 | GSE225456 | GEO

Spatial transcriptome sequencing of primary nasopharyngeal carcinoma tissues

Project description:Spatial transcriptome sequencing of primary nasopharyngeal carcinoma tissues

| PRJNA824039 | ENA

standR: spatial transcriptomic analysis for GeoMx DSP data.

Project description:To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of the subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here, we present standR, an R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how the application of standR enables scientists to develop in-depth insights into the biology of interest.

| S-EPMC10783521 | biostudies-literature

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data