GeoMx® Mouse Whole Transcriptome Atlas

Helping Your Research

Full Transcriptome Spatial RNA Analysis

Mouse models serve a critical role in understanding developmental biology, disease onset, progression, and treatment.  Tissue heterogeneity, however, confounds the results from many mouse transcriptome studies based on bulk or single cell RNA-seq data.  Using the GeoMx Mouse Whole Transcriptome Assay, one can apply spatial transcriptomics to reveal the tissue architecture and underlying function in genetically modified mouse models.

How it Works


Superior Sensitivity Detects More Genes per Sample


Robust, reproducible results across sample types including FFPE, Frozen Fresh, Fixed Frozen, and TMAs


Designed for All Major Mouse Strains


Efficiently compare data across multiple samples to identify changes in biologically relevant compartments or cell populations

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Publications & Posters

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Characterizing Late-Onset AD Models Using Spatial Whole Transcriptome Analysis – AGBT 2021

Smarca4-deficient lung cancers display a metastatic-like cell state and a distinct cell-of-origin – AGBT 2021

Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma

Synovial sarcoma (SyS) is an aggressive neoplasm driven by the SS18-SSX fusion, and is characterized by low T cell infiltration. Here, we studied the cancer-immune interplay in SyS using an integrative approach that combines single-cell RNA sequencing (scRNA-seq), spatial profiling and genetic and pharmacological perturbations.

The spatial landscape of lung pathology during COVID-19 progression

Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1–8. However, thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking.

Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection

The relationship of SARS-CoV-2 pulmonary infection and severity of disease is not fully understood. Here we show analysis of autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter-patient and intra-patient heterogeneity of pulmonary virus infection.

Related Resources

See All Resources
Product Bulletin GeoMx Mouse Whole Transcriptome Atlas – Product Bulletin
Whitepaper The GeoMx® Whole Transcriptome Atlas for the Digital Spatial Profiler: Design, Performance, and Experimental Guidelines – Whitepaper
App Note/Tech Note Ultra-High-Plex Spatial Proteogenomics of FFPE Tissue Sections
Gene Targets Access the GeoMx Mouse Whole Transcriptome Atlas via UCSC Genome Browser
Manual/Instructions GeoMx® DSP: Data Analysis for NGS Readout

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