GeoMx DSP services: spatial RNA & high-plex proteomics by region and compartment
Explicyte delivers GeoMx DSP studies across selected tissue regions and compartments, combining RNA, high-plex protein and RNA–protein multiomic workflows with in-house analysis.
GeoMx data generated by Explicyte have been published in
GeoMx CRO services
Why run GeoMx with Explicyte
GeoMx experience, certified provider since 2020
Explicyte is a certified NanoString partner (now part of Bruker Spatial Biology) with years of GeoMx experience and a peer-reviewed publication track record across translational oncology.
Flexible ROI & compartment selection
Define the tissue regions that matter, with ROI/AOI selection based on your own criteria, pathologist input, or developed jointly with the Explicyte team.
Spatial RNA + high-plex proteomics
Profile broad RNA programs, high-plex protein expression and signaling states, or combine both modalities within selected spatial regions
HOW WE RUN GEOMX STUDIES
From study design to compartment-resolved molecular data
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1Study design & ROI/AOI strategy
A PhD study director reviews your biological objectives, cohort and available tissue, then defines the molecular readout and ROI/AOI strategy with your team. Depending on the study, this can include WTA, CTA, high-plex protein profiling or an integrated RNA–protein workflow. ROI/AOI criteria can be sponsor-defined, Explicyte-defined or jointly established. -
2Samples, preparation, and QC
We provide sample and shipping requirements and can support tissue sourcing where needed. FFPE or fresh-frozen material is prepared and qualified according to the selected RNA or protein assay before proceeding to GeoMx profiling.
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3Imaging, ROI/AOI selection & molecular readout
Sections are stained with fluorescent morphology markers together with assay-specific RNA probes and/or oligo-tagged antibodies. After imaging, ROIs and AOIs are selected according to the predefined study strategy, either by the sponsor team, Explicyte or collaboratively. UV illumination then releases the indexing oligos from each selected area for downstream molecular readout.
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4Data processing, analysis & delivery
Raw outputs include FASTQ and DCC files. Our in-house data science team can then perform QC, normalization, differential RNA and/or protein expression, pathway and signature analysis, immune-cell deconvolution where appropriate, compartment comparisons and integrated RNA–protein analysis.
GEOMX ASSAYS & SPECIFICATIONS
Spatial RNA, high-plex proteomics & multiomics
- Readout principle
- Study-defined regions of interest (ROIs) and areas of illumination (AOIs), selected using tissue morphology and fluorescent markers—for example tumor versus stroma or selected immune compartments.
- RNA content
- Whole Transcriptome Atlas — 18,000+ protein-coding genes, human or mouse. Cancer Transcriptome Atlas — 1,800+ targets across cancer-related pathways.
- IO Proteome Atlas
- 570+ human protein targets for broad immuno-oncology and translational biomarker discovery, with up to 40 additional custom protein targets.
- Discovery Proteome Atlas
- 1,200+ pre-validated human protein targets, including 130+ post-translational modifications.
- Spatial multiomics
- Integrated RNA–protein study designs combining GeoMx transcriptomic and high-plex protein assays, with workflow configuration depending on the selected assay combination.
- Sample types
- FFPE, fresh-frozen and TMAs, including biopsies. Compatibility depends on the selected RNA or protein assay.
- Morphology guidance
- Up to four fluorescent morphology channels to guide ROI/AOI selection and compartment enrichment.
- Certification
- NanoString Certified Service Provider for GeoMx DSP, now part of Bruker Spatial Biology.
GeoMx data & analysis deliverables
Raw & standard outputs
- FASTQ and DCC files for NGS-based workflows
- ROI/AOI annotations and QC metrics
- Normalized RNA and/or protein expression matrices
Downstream analysis, according to study scope
- Differential RNA and/or protein expression
- Pathway and gene-set analysis
- Protein-signaling and PTM analysis where applicable
- Immune-cell deconvolution where relevant
- Tumor-versus-stroma and other compartment-level comparisons
- Integrated RNA–protein analysis for spatial multiomic studies
Study outputs
- Processed datasets
- Publication-ready figures
- Results review with your study director
Peer-reviewed studies using Explicyte GeoMx data
Explore our GeoMx publications
Adenosine A2B Receptor Promotes Tumor Progression and Metastases in Undifferentiated Pleomorphic Sarcoma
Spatially resolved transcriptomics reveal the determinants of primary resistance to immunotherapy in NSCLC with mature tertiary lymphoid structures
Identification of microenvironment features associated with primary resistance to anti-PD-1/PD-L1 + antiangiogenesis in gastric cancer through spatial transcriptomics and plasma proteomics
Upregulation of Indoleamine 2,3-Dioxygenase 1 in Tumor Cells and Tertiary Lymphoid Structures is a Hallmark of Inflamed Non–Small Cell Lung Cancer
Pembrolizumab in soft-tissue sarcomas with tertiary lymphoid structures: a phase 2 PEMBROSARC trial cohort
Spatial transcriptomics of macrophage infiltration in non-small cell lung cancer reveals determinants of sensitivity and resistance to anti-PD1/PD-L1 antibodies
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your GeoMx project
Tell us your tissue type, cohort size, biological question and desired RNA or protein readout. We'll help define the appropriate GeoMx assay, ROI/AOI strategy, sample requirements and analysis plan.
Frequently asked questions about GeoMx DSP services
GeoMx FAQs
What is GeoMx digital spatial profiling?
GeoMx Digital Spatial Profiling measures RNA and/or protein expression within selected regions of tissue. ROIs and AOIs are defined using tissue morphology and fluorescent markers and can follow sponsor-defined criteria, Explicyte-defined study rules or a jointly agreed selection strategy. Depending on the study, GeoMx can profile whole-transcriptome RNA, targeted RNA content, high-plex protein expression or integrated RNA–protein spatial multiomics.
When should I use GeoMx rather than Xenium or Visium HD?
GeoMx is particularly useful when the biological question focuses on molecular profiling of selected tissue regions or compartments—for example tumor, stroma or defined immune-rich areas—and when RNA, protein or both need to be measured within those regions.
Visium HD is better suited to broad whole-transcriptome spatial discovery across tissue, while Xenium provides targeted cell-resolved and subcellular RNA localization.
GeoMx is especially differentiated by flexible ROI/AOI selection, high-plex proteomics and RNA–protein multiomic study designs.
How is GeoMx different from Atera?
GeoMx profiles selected ROIs/AOIs and can combine spatial RNA with high-plex protein measurements.
Atera profiles whole-transcriptome RNA directly across tissue at single-cell sensitivity.
The choice therefore depends on whether the study prioritizes selected-region profiling and protein biology or broad in situ transcriptomic coverage.
Is GeoMx a single-cell method?
GeoMx is primarily a region- and compartment-based spatial profiling technology. RNA workflows such as WTA and CTA typically measure selected ROIs/AOIs rather than generating an unbiased cell-by-cell map of the tissue. Some high-plex protein workflows can interrogate very small or highly enriched cellular regions depending on study design, but GeoMx should not be presented as equivalent to whole-tissue single-cell imaging platforms.
How are GeoMx ROIs and AOIs selected?
ROI/AOI selection is defined during study design and can be performed by the sponsor team, by Explicyte or collaboratively. Fluorescent morphology markers are used to identify relevant tissue structures or cellular compartments—for example tumor versus stroma or selected immune-rich regions. Pathologist input can be incorporated when histological interpretation is useful, but it is not required for every GeoMx study.
What GeoMx RNA and protein assays are available?
For RNA, Explicyte offers the Whole Transcriptome Atlas with 18,000+ protein-coding genes and the Cancer Transcriptome Atlas with 1,800+ cancer-related targets. For protein profiling, the IO Proteome Atlas measures 570+ human proteins, while the Discovery Proteome Atlas expands coverage to 1,200+ proteins, including 130+ post-translational modifications. DPA can also be customized with up to 40 additional protein targets.
Can GeoMx measure RNA and protein on the same tissue section?
Yes, depending on the selected assay combination and study design. GeoMx supports integrated RNA–protein workflows, including same-section or matched-section approaches depending on the assays used. We define the appropriate configuration during study setup
What is the GeoMx Discovery Proteome Atlas?
The GeoMx Discovery Proteome Atlas (DPA) is a 1,200+ plex antibody-based spatial proteomics assay for human tissue. Its curated targets span major signaling and disease pathways and include 130+ post-translational modifications. DPA can resolve protein expression and can be integrated with GeoMx WTA for spatial RNA–protein analysis.
Why are post-translational modifications useful?
RNA expression does not always reflect functional pathway activity. DPA includes 130+ post-translational modifications, including phosphorylation and other regulatory protein states, allowing studies to investigate signaling activity directly in spatially defined tissue compartments. This can be particularly valuable for mechanism-of-action studies, target discovery and pharmacodynamic biomarker research.
What samples do you accept?
GeoMx studies can support FFPE and fresh-frozen tissue, including biopsies and TMAs. Compatibility depends on the selected RNA or protein assay and species. We review sample type, tissue dimensions and material quality during study setup.
How is the readout generated?
After region selection, UV light releases barcoded oligos from each segment; those are collected and read out by NGS (Illumina).
What do I receive at the end?
Depending on study scope, deliverables can include FASTQ and DCC files, ROI/AOI annotations and QC, normalized RNA and/or protein expression matrices, differential expression, compartment-level comparisons, pathway and signaling analyses, immune-cell deconvolution where appropriate, and integrated RNA–protein analyses. Processed datasets and publication-ready figures can be reviewed with your study director.
Are you certified for GeoMx?
Explicyte has been a certified NanoString partner since 2020 (now part of Bruker Spatial Biology) and runs GeoMx DSP directly.
