GeoMx DSP Morphology Marker Reference List

As part of the GeoMx® Digital Spatial Profiler (DSP) workflow, fluorescently-labeled morphology markers (MM) are used for visualization of tissue morphology, selection of regions of interest (ROI), and segmentation of ROIs into distinct biological compartments, or areas of illumination (AOI). 

Many GeoMx DSP researchers find that the off-the-shelf kits provided by NanoString (listed in tab 2. GeoMx MM Kits) achieve sufficient tissue labeling for precise spatial profiling without the time and expense of de novo morphology marker optimization.

If other morphology markers are required for your project, refer to tabs 3. Human MM, 4. Mouse MM, and 5. Canine MM for lists of antibodies tested by NanoString for compatibility with the GeoMx slide preparation protocols. Antibodies tested by the NanoString Technology Access Program (TAP) have been qualified to work with customer-provided tissue for at least one project.  NanoString R&D-tested antibodies fall into two categories: Qualified markers have passed an initial screening using a standardized staining concentration, antigen retrieval parameters, and assay conditions.  Verified markers have been further refined with the tissue(s) indicated.

The GeoMx development team has integrated Advanced Cell Diagnostics (ACD) RNAscope® protocols for use with GeoMx RNA assays. Compatible morphology markers are listed in tab 6. RNAScope-compatible. While the protocols have been validated, each tissue type, RNAscope target and fluorescent channel may need to be optimized for desired performance. In addition, proper RNAscope controls should be used to assess the quality of RNAscope probes.

Tab 7. Spatial Organ Atlas MM lists the antibody clones and commercial vendor information for experiments comprising NanoString's Spatial Organ Atlas.

The antibody concentrations, sample prep conditions, and scan exposure times given here are a good starting point.  Optimization by the user for their particular experiment, combination of morphology markers and tissue may be required.  Any research or development performed by you with these morphology markers is done entirely at your own risk and NanoString is not responsible for any errors, failures, sample loss, or data loss resulting from your use of these antibodies. The information contained herein is provided as a reference tool only and NanoString makes no recommendation or endorsement regarding the use of any antibodies referenced in this document. These morphology markers are available for purchase directly from third party vendors. Aside from NanoString's Morphology Marker Kits, NanoString does not provide or sell these antibodies or RNAscope probes.  RNAscope probes are available for purchase directly from ACD. 

For more information on morphology markers and their optimization, refer to the NanoString website:
https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-morphology-markers/