GeoMx

The GeoMx Digital Spatial Profiler (DSP) from 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 or computationally elucidate 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 counted on an nCounter platform (NanoString). The resulting counts constitute an expression or protein profile of key targets across that ROI and elucidate the biology specific to that region. In addition, TRIP Lab, in collaboration with the UWBC Gene Expression Center (GEC) is excited to offer GeoMx with NGS readout which allows the spatial and molecular profiling of 1,800 targets to 18,000 targets in one single tissue slide.

For GeoMx questions and to schedule a meeting to discuss your project and timeline, contact the TRIP Lab at trip@pathology.wisc.edu or 608-265-9168.

For pricing please see our TRIP Fee Schedule.

To request GeoMx DSP services, go to our iLab webpage.

FAQs

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What type of sample can I use for Nanostring 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?

What type of targets can I use in my Nanostring GeoMx DSP experiment?

-Protein 

-RNA 

 

What type of regions of interest (ROI) can I select for my project?

You can select either automated or customized region of interest (ROI) algorithms based on the true biology of the sample. From tumor and microenvironment down to the single cell resolution, flexible selection allows you to get to answers faster. 

What type of quantitative assays are compatible with Nanostring GeoMx DSP?

Nanostring nCounter (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 Nanostring GeoMx DSP project look like?

Alternatively, on Day 3 samples may be taken to the Biotech Gene Expression Center for Next Generation Sequencing. 

How does GeoMx DSP data look like?

What types of morphology markers are available?

What type of protein panels are available?

What is included in the Transcriptome Atlas Portfolio?

What is SpatialDecon algorithm and what are its applications?

SpatialDecon is an algorithm for quantifying mixed cell types in the regions of GeoMx experiments. It requires a pre-specified matrix of cell type expression profiles; easily generated from scRNAseq. For more information go here: https://www.biorxiv.org/content/10.1101/2020.08.04.235168v1.full.pdf

Uses:

-How are cell types arranged and mixed with each other?

-Which cell types repel or attract each other?

-Which cell types explain the expression patterns of a gen of interest?

-How does a cell population behavior change when it is co-localized with another cell population?