The equipment in the Spatial Biology Recharge Facility includes:

GeoMx option 1

The GeoMx Digital Spatial Profiler (DSP) is a new NanoString Technologies platform that determines the quantity of proteins and messenger RNA in tissue. Messenger RNA is a molecule that receives genetic instructions from DNA and creates proteins that carry out functions within cells.

The profiler uses unique reagents in the form of antibodies or RNA probes coupled to ultraviolet (UV) photocleavable oligonucleotide bar codes. The bar codes enable the light-dependent changes of biomolecular activities with great precision. Then the DSP scans the slides and gives high-quality images.

Focused UV light based on which region and segment of the tissue the user selects releases the oligonucleotide, which is a short DNA and RNA molecular tag. The DSP instrument tunes the UV light to make region selection more flexible, including selecting irregularly shaped and noncontinuous segments. The nCounter optical bar codes or an Illumina next-generation sequencer measures the quantity of released tags. Finally, the DSP maps the counts back to the tissue location, resulting in a spatially resolved digital profile of protein or messenger RNA abundance.

GeoMx option 2

This service determines the quantity of target proteins and transcripts in a slide. It allows for cell type-specific analysis of frozen, paraffin-embedded tissues and formalin-fixed and paraffin-embedded (FFPE) tissues.

The GeoMx Digital Spatial Profiler detects target proteins or RNA species using antibodies or crossbreeding probes that join to indexing oligos using a UV-cleavable linker. This cleavable linker can be split. Localized digital UV illumination releases the oligos from the slide. This step gives spatial information for each sample. An automated capillary pipette collects the released oligos from a watery layer above the tissue slice over each region of interest. Then it transfers the collection into microwells for index counting.

The last step can use NanoString Technologies' nCounter technology, also called next-generation sequencing, which allows a nearly endless degree of multiplexing. Note that the original tissue is not destroyed because the UV-cleaved index oligos are recovered while the original proteins and RNA remain in place.


This is NanoString Technologies' molecular bar coding technology, which uses color-coded molecular bar codes that can crossbreed to many types of target molecules. It is ideal for applications that need to efficiently and precisely measure the quantity of up to 800 target molecules across a sample set. The nCounter technology produces high-quality results from challenging sample types, including FFPE and crude cell lysates.

Narrator: Gene expression analysis is a powerful tool for measuring biological processes that underlie disease progression and therapeutic effectiveness.

However, analyzing RNA using traditional technologies requires complex steps to convert RNA to cDNA which is then amplified and quantified as a proxy for the original RNA.

This process introduces variability which may lead to biased data and an inability to replicate results.

Why introduce and count cDNA errors when you can simply count the native RNA?

Direct detection using nCounter technology provides highly robust data across clinically relevant samples while reducing hands-on time and simplifying analysis.

nCounter technology gets you to reproducible results faster.

Using molecular barcode technology RNA is directly tagged with a capture probe and a reporter probe that are specific to the target of interest creating a unique target-probe complex.

After hybridization, excess probes are removed leaving only purified target-probe complexes.

These complexes are immobilized and aligned on the imaging surface.

The sample is then scanned by an automated fluorescence microscope where labeled barcodes are directly counted, and the data analyzed through an intuitive analysis software.

Molecular barcoding technology can be used with RNA, miRNA, protein, and DNA analytes.

Direct detection with nCounter technology provides several advantages:

  • Highly Reproducible Data - Across multiple users and sites.
  • Robust Performance - On FFPE samples.
  • Single Tube Multiplexing - Up to 800 RNA targets in a single tube.
  • Simple Protocol - Less than 15 minutes of hands-on time.
  • Flexible Sample Input.
  • Simple Data Analysis - Publication ready figures in hours.

Faster than NGS. Simpler than qPCR.

Direct detection with nCounter technology by NanoString.