The GeoMx Digital Spatial Profiler (DSP) from Bruker Spatial Biology (formerly known as NanoString), is a technology that enables high-plex spatial and molecular analysis of RNA and protein in tissue specimens on slides. Tissue slides are stained with large panels of pre-mixed biological probes, which each contains a unique, UV-cleavable DNA barcode; and fluorescently-labeled morphology markers to visually the morphology of the tissue. Using the morphology markers for guidance, then ROIs are selected and are illuminated with UV light. The cleaved barcodes from these ROIs are then collected and counted on an nCounter platform (Bruker Spatial Biology). The resulting counts constitute an expression or protein profile of key targets across that ROI and illustrate the biology specific to that region. Alternatively, TRIP Lab, in collaboration with the UWBC Gene Expression Center (GEC) offers GeoMx with NGS readout allowing the spatial and molecular profiling >18,000 targets on a single slide.
For GeoMx questions and to schedule a meeting to discuss your project, contact the TRIP Lab at trip@pathology.wisc.edu.
To request GeoMx DSP services, go to our iLab webpage.
Use this Handbook as a guide to prepare your GeoMx Project.
GeoMx FAQ
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What QC needs to be done on my samples?
The GeoMx DSP workflow begins with tissue QC to assess RNA quality using ACD’s RNAscope® Multiplex Fluorescent Reagent Kit in combination with a species-specific positive control probe. If the tissue does not express an adequate amount of quality RNA based on ACD’s positive control scale, it is not suitable for GeoMx. The positive control probes that make up the multiplex probe have been selected due to their abundance in nearly every tissue type.
These are images are taken from two TMAs of the same tissue type where the cores used to make Block 1 were from samples 12-23 years old at the time of staining and cores used to make Block 2 were from samples 7-13 years old. We ran FISH RNA QC on both to determine which would be a better fit for GeoMx. Based on the RNAscope Multiplex Fluorescent Reagent kit results, Block 2 was the preferred choice for GeoMx, demonstrating higher overall RNA expression and stronger correlation with the expected per-cell expression for both UBC and PPIB positive control probes.
TMA 1: 14-22 yrs old cores TMA 2: 8-12 years old cores
Additionally, the GeoMx WTA panel was run on slides from both TMA blocks. The slide from the older samples in Block 1 produced no usable data, while the slide on the right did.
What type of sample can I use for GeoMx DSP?
With this technology you can use: formalin-fixed paraffin-embedded (FFPE) tissue, fresh frozen tissue, or microarrays (TMAs).
How should I prepare my sample?
Please follow the following guides for sample and slide preparation. If you have questions, please contact TRIP lab prior to harvesting your tissue.
Sample and Slide Preparation: Sample Prep Guidelines
Fresh Frozen Samples for RNA analysis
What type of targets can I use in my GeoMx DSP experiment?
-Protein
-RNA
What type of quantitative assays are compatible with GeoMx DSP?
–Bruker Spatial Biology (formerly NanoString) nCounter Readout (available at TRIP). Check our nCounter MAX page for more information.
–Next Generation Sequencing (NGS, in collaboration with UWBC).
What does the workflow of a GeoMx DSP project look like?
Alternatively, on Day 3 samples may be taken to the Biotech Gene Expression Center for Next Generation Sequencing.
Can I used expired GeoMx reagents?
TRIP does not work with expired GeoMx reagents. For that reason, you don’t want to order your reagents too early. Wait until TRIP staff has given you the ok to purchase reagents. Some reagents we may have on hand at a discounted rate.
Contact Becky at: rmbaus@wisc.edu for more details on what is available.
What does GeoMx DSP data look like?
Publications:
Williams, A.E., Hoffmann, E.J., Inman, D.R. et al. Obesity and breast density enhance immune exclusion in the primary tumor microenvironment and promote breast cancer metastasis. Oncogene (2026). https://doi.org/10.1038/s41388-026-03718-8
Rastogi I, McNeel DG. Prostate tumor immune microenvironment changes following immunotherapy shared by patients who developed anti-tumor response or immune-related adverse events. Oncoimmunology. 2025 Dec 31;14(1):2595788. doi: 10.1080/2162402X.2025.2595788. Epub 2025 Dec 11. PMID: 41378786; PMCID: PMC12710901.
Zhang X, Lan R, Liu Y, Pillarisetty VG, Li D, Zhao CL, Sarkar SA, Liu W, Hanna I, Gupta M, Hajdu C, Melamed J, Shusterman M, Widmer J, Allendorf J, Liu YZ. Complement activation in tumor microenvironment after neoadjuvant therapy and its impact on pancreatic cancer outcomes. NPJ Precis Oncol. 2025 Mar 3;9(1):58. doi: 10.1038/s41698-025-00848-2. PMID: 40032924; PMCID: PMC11876354.
Damodharan S, Shireman JM, Xie E, Distler E, Kendziorski C, Dey M. Transcriptomic and proteomic spatial profiling of pediatric and adult diffuse midline glioma H3 K27-Altered. Sci Rep. 2024 Sep 30;14(1):22668. doi: 10.1038/s41598-024-73199-w. PMID: 39349581; PMCID: PMC11443003.
Zhang X, Lan R, Liu Y, Pillarisetty VG, Li D, Zhao CL, Sarkar SA, Liu W, Hanna I, Gupta M, Hajdu C, Melamed J, Shusterman M, Widmer J, Allendorf J, Liu YZ. Enhanced Complement Expression in the Tumor Microenvironment Following Neoadjuvant Therapy: Implications for Immunomodulation and Survival in Pancreatic Ductal Adenocarcinoma. Res Sq [Preprint]. 2024 May 13:rs.3.rs-4104258. doi: 10.21203/rs.3.rs-4104258/v1. PMID: 38798691; PMCID: PMC11118688.
Poster: Paz, Cristina, Annemarie Glassey, Abigail Frick, Lauryn Melzer, Jasmine M. Robinson, Rebecca M. Baus, Randall J. Kimple. Abstract 7446: Transcriptomic and histological analysis of radiation-induced damage in the murine submandibular gland. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl): Abstract nr 7446.
Faralli JA, Filla MS, Yang YF, Sun YY, Johns K, Keller KE, Peters DM. Digital spatial profiling of segmental outflow regions in trabecular meshwork reveals a role for ADAM15. PLoS One. 2024 Feb 23;19(2):e0298802. doi: 10.1371/journal.pone.0298802. PMID: 38394161; PMCID: PMC10889904.
Lozar, T,; Laklouk, I.; Golfinos, A.E.; Gavrielatou, N., Xu, J.; et al. Stress Keratin 17 Is a Predictive Biomarker Inversely Associated with Response to Immune Check-Point Blockade in Head and Neck Squamous Cell Carcinomas and Beyond. Cancers. 2023, Oct, 9.
Resources:
Seminar PowerPoint: Functional Spatial Multiomics with GeoMx DSP: Integrating Biological Layers to Advance Mechanistic Biomarker Discovery. Hosted by TRIP Lab & Bruker Spatial Biology. Speakers: Grant Barthel (Bruker), Karla Esbona, PhD (TRIP Lab), Sheena Kerr, PhD (David Beebe Lab), March 25, 2026.
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