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?
It has been shown that running ACD’s RNAscope FISH using their multiplex positive control probe provides the level of quality RNA expression of each of your samples . 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 different TMAs where the blocks used to make them had been grouped in such a way that the older blocks were all put on one TMA and the newer blocks on the other. In running FISH on both, we found the RNA expression level to be much higher on the image to the right, with the younger blocks. Additionally, we ran the GeoMx WTA panel on both of the slides. The slide on the left produced no usable data, while the slide on the right did.
blocks 14-22 yrs old blocks 8-12 years old
Kerr, Beebe 2024
What type of sample can I use for GeoMx DSP?
With this technology you can use any sample type from formalin-fixed paraffin-embedded (FFPE) tissue, to fresh frozen tissue to tissue microarrays (TMAs).
How should I prepare my sample?
Please follow the following guides for sample and slide preparation.
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:
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.
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:
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