Spatial RNA and protein profiling

The GeoMX Digital Spatial Profiler (DSP) is a cutting-edge platform that enables high-resolution spatial profiling of proteins and RNA within tissue samples. Using ultraviolet (UV) light and barcoded oligonucleotide probes attached to antibodies or RNA targets, GeoMX precisely maps the expression of hundreds of molecules across regions of interest (ROIs) in variety of complex tissues, such as tumors or brain sections.

After selecting specific ROIs, based on morphology markers fluorescent staining, UV light releases the barcoded probes from the tissue, which are then collected and quantified using nCounter or next-generation sequencing (NGS). The technology allows researchers to study molecular interactions in situ while preserving the spatial context, providing valuable insights into tissue heterogeneity and disease pathology.

​Sample Preparat​​ion

Tissue sections are prepared and mounted on slides, then stained with fluorescently labeled antibodies or RNA probes targeting specific proteins or transcripts.

Region of Interest (ROI) Selection

Using the GeoMX platform's high-resolution imaging, specific regions of interest (ROIs) within the tissue are selected, based on morphological markers.

UV Light Cleavage

UV light is directed to the selected ROIs, releasing barcoded oligonucleotide tags attached to the probes, while preserving the tissue architecture.

Barcode Collection & Quantification

The released barcodes are collected and quantified using next-generation sequencing (NGS) or digital counting, providing spatially resolved data for protein or RNA expression.

Data Analysis

The quantified molecular data are analyzed, correlating spatial expression patterns with tissue architecture, disease states, or other biological features.​

Consultation

Schedule a consultation with the core facility team to discuss project feasibility, experimental design, and assay selection. Academic and collaborative projects with common publications are prioritized.

Project Proposal

Submit a detailed project proposal outlining objectives, tissue types, RNA or protein profiling, and specific regions of interest (ROIs) to be analyzed.

Sample Submission

Ensure samples are properly prepared and meet GeoMX requirements (e.g., tissue type, thickness, fixation) before submission.

Data Ownership

Data generated from collaborative projects will be shared with the project PI. Any publication or presentation must acknowledge the GeoMX core facility.

Cost Sharing

Collaborators are responsible for costs associated with time used (staff scientist and bls), reagents, sequencing, and data analysis, as agreed upon before project initiation.

Timeline

Projects are processed on a first-come, first-served basis. Estimated timelines will be provided during consultation.

Authorship

Core facility staff contributing substantially to experimental design, data acquisition, or analysis should be considered for co-authorship in publications.

Data Storage

Raw data will be stored for a fixed period (e.g., 6 months) after the project is completed; long-term storage is the responsibility of the collaborator.​

​Harwood, D.S.L., Pedersen, V., Bager, N.S. et al. Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue. Nat Commun 15, 7857 (2024).​

Tekin H, Lindhardt C, Antvorskov JC, Bager NS, Michaelsen SR, Areškevičiūtė A, Vind JP, Kristensen BW, Josefsen K. Using GeoMx DSP Spatial Proteomics to Investigate Immune Infiltration of NOD Mouse Islet and Exocrine Compartments. Mol Imaging Biol. 2024 Nov 18. doi: 10.1007/s11307-024-01961-7. Epub ahead of print. PMID: 39557779.​

Puig-Blasco L, Piotrowski KB, Michaelsen SR, et al. Loss of cancer cell-derived ADAM15 alters the tumor microenvironment in colorectal tumors. Int J Cancer. 2023; 153(12): 2068-2081. doi:10.1002/ijc.34695.