GeoMx™ RNA Assay: High Multiplex, Digital, Spatial Analysis of RNA in FFPE Tissue

Methods Mol Biol. 2020:2148:331-345. doi: 10.1007/978-1-0716-0623-0_21.


RNA in situ hybridization (ISH) is a widely used technique for the localization of mRNA in tissues. Limitations to traditional ISH include the number of targets that can be analyzed concurrently and the ability for many of these assays to be used in formalin-fixed, paraffin-embedded tissues (FFPE). Here, we describe the GeoMx™ RNA assay that is capable of the highly multiplexed detection of mRNA targets in FFPE tissues. This assay utilizes ISH probes linked to indexing oligo barcodes via a photocleavable linker and the GeoMx Digital Spatial Profiler (DSP) Instrument to enable profiling of RNA targets in a region-of-interest-based method. In brief, 5 μm FFPE sections are dewaxed, target retrieved, digested with proteinase K, post-fixed, and then incubated overnight with GeoMx RNA detection probes. Stringent washes are performed followed by the addition of fluorescently labeled antibodies for use as morphology markers. User-defined regions of interest are then profiled on the GeoMx DSP through region-specific cleaving and collecting the photocleaved indexing oligos. Cleaved indices are then quantified using NanoString nCounter® Technology generating digital quantification of RNA expression with spatial context.

Keywords: FFPE; Genomics; GeoMx DSP; High-plex; ISH; Profiling; Spatial.

MeSH terms

  • Gene Expression Profiling / methods*
  • Humans
  • In Situ Hybridization / methods*
  • Paraffin Embedding / methods
  • RNA / genetics*
  • RNA / isolation & purification
  • Spatial Analysis
  • Tissue Fixation / methods


  • RNA